A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Ribonucleic acid that makes up the genetic material of viruses.
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
The relationships of groups of organisms as reflected by their genetic makeup.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
Viruses whose genetic material is RNA.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.
The processes of RNA tertiary structure formation.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The functional hereditary units of BACTERIA.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
A family of proteins that promote unwinding of RNA during splicing and translation.
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Proteins found in any species of bacterium.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
RNA present in neoplastic tissue.
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Established cell cultures that have the potential to propagate indefinitely.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.
A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function.
Deoxyribonucleic acid that makes up the genetic material of viruses.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The sum of the weight of all the atoms in a molecule.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
Any method used for determining the location of and relative distances between genes on a chromosome.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
The functional hereditary units of VIRUSES.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Genotypic differences observed among individuals in a population.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
Proteins prepared by recombinant DNA technology.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
Small, linear single-stranded RNA molecules functionally acting as molecular parasites of certain RNA plant viruses. Satellite RNAs exhibit four characteristic traits: (1) they require helper viruses to replicate; (2) they are unnecessary for the replication of helper viruses; (3) they are encapsidated in the coat protein of the helper virus; (4) they have no extensive sequence homology to the helper virus. Thus they differ from SATELLITE VIRUSES which encode their own coat protein, and from the genomic RNA; (=RNA, VIRAL); of satellite viruses. (From Maramorosch, Viroids and Satellites, 1991, p143)
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
Deoxyribonucleic acid that makes up the genetic material of fungi.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Biochemical identification of mutational changes in a nucleotide sequence.
The rate dynamics in chemical or physical systems.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
The small RNAs which provide spliced leader sequences, SL1, SL2, SL3, SL4 and SL5 (short sequences which are joined to the 5' ends of pre-mRNAs by TRANS-SPLICING). They are found primarily in primitive eukaryotes (protozoans and nematodes).
In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
Viruses parasitic on plants higher than bacteria.
Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
The functional hereditary units of FUNGI.
A reaction that severs one of the sugar-phosphate linkages of the phosphodiester backbone of RNA. It is catalyzed enzymatically, chemically, or by radiation. Cleavage may be exonucleolytic, or endonucleolytic.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.
Nuclear nonribosomal RNA larger than about 1000 nucleotides, the mass of which is rapidly synthesized and degraded within the cell nucleus. Some heterogeneous nuclear RNA may be a precursor to mRNA. However, the great bulk of total hnRNA hybridizes with nuclear DNA rather than with mRNA.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
The steps that generate the 3' ends of mature RNA molecules. For most mRNAs (RNA, MESSENGER), 3' end processing referred to as POLYADENYLATION includes the addition of POLY A.
Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.
Short RNA, about 200 base pairs in length or shorter, that does not code for protein.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Proteins obtained from ESCHERICHIA COLI.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Transport proteins that carry specific substances in the blood or across cell membranes.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
Diseases of plants.
Proteins encoded by a VIRAL GENOME that are produced in the organisms they infect, but not packaged into the VIRUS PARTICLES. Some of these proteins may play roles within the infected cell during VIRUS REPLICATION or act in regulation of virus replication or VIRUS ASSEMBLY.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Sequential operating programs and data which instruct the functioning of a digital computer.
Proteins found in any species of virus.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
Proteins that form the CAPSID of VIRUSES.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.
Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.
Proteins found in any species of fungus.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.

In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron. (1/3208)

The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual twin-ribozyme organization. One of the ribozymes (DiGIR2) catalyses intron excision and exon ligation. The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open reading frame (ORF) is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1 and IPS2) located at its 3' end. Examination of the in vivo expression of DiSSU1 shows that after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed cleavage upstream of the ORF 5' end, as well as truncation and polyadenylation downstream of the ORF 3' end. A spliceosomal intron, the first to be reported within a group I intron and the rDNA, is removed before the I-DirI mRNA associates with the polysomes. Taken together, our results imply that DiSSU1 uses a unique combination of intron-supplied ribozyme activity and adaptation to the general RNA polymerase II pathway of mRNA expression to allow a protein to be produced from the RNA polymerase I-transcribed rDNA.  (+info)

Nucleotide sequences and taxonomy of satsuma dwarf virus. (2/3208)

The nucleotide sequences of genomic RNA1 (6795 nt) and RNA2 (5345 nt) of satsuma dwarf virus (SDV), a tentative member of the genus Nepovirus, were determined. The deduced genome organization of SDV showed similarities to the organization in como-, faba- and nepoviruses. There is extensive amino acid sequence similarity in the N-terminal regions of the proteins encoded by RNA1 and RNA2, as reported previously only for tomato ringspot nepovirus. However, unlike definitive nepoviruses, which have a single coat protein, SDV has two coat proteins. SDV RNA2 does not contain the long (> 1300 nt) 3' non-coding region characteristic of some nepoviruses. Phylogenetic analysis of SDV RNA polymerase placed SDV apart from como-, faba- and nepoviruses. These unique features suggest that SDV is distinct from the Comovirus, Fabavirus and Nepovirus genera, and needs to be separated into a new genus, probably within the family Comoviridae.  (+info)

Degradation of 1,2-dibromoethane by Mycobacterium sp. strain GP1. (3/3208)

The newly isolated bacterial strain GP1 can utilize 1, 2-dibromoethane as the sole carbon and energy source. On the basis of 16S rRNA gene sequence analysis, the organism was identified as a member of the subgroup which contains the fast-growing mycobacteria. The first step in 1,2-dibromoethane metabolism is catalyzed by a hydrolytic haloalkane dehalogenase. The resulting 2-bromoethanol is rapidly converted to ethylene oxide by a haloalcohol dehalogenase, in this way preventing the accumulation of 2-bromoethanol and 2-bromoacetaldehyde as toxic intermediates. Ethylene oxide can serve as a growth substrate for strain GP1, but the pathway(s) by which it is further metabolized is still unclear. Strain GP1 can also utilize 1-chloropropane, 1-bromopropane, 2-bromoethanol, and 2-chloroethanol as growth substrates. 2-Chloroethanol and 2-bromoethanol are metabolized via ethylene oxide, which for both haloalcohols is a novel way to remove the halide without going through the corresponding acetaldehyde intermediate. The haloalkane dehalogenase gene was cloned and sequenced. The dehalogenase (DhaAf) encoded by this gene is identical to the haloalkane dehalogenase (DhaA) of Rhodococcus rhodochrous NCIMB 13064, except for three amino acid substitutions and a 14-amino-acid extension at the C terminus. Alignments of the complete dehalogenase gene region of strain GP1 with DNA sequences in different databases showed that a large part of a dhaA gene region, which is also present in R. rhodochrous NCIMB 13064, was fused to a fragment of a haloalcohol dehalogenase gene that was identical to the last 42 nucleotides of the hheB gene found in Corynebacterium sp. strain N-1074.  (+info)

Salmon pancreas disease virus, an alphavirus infecting farmed Atlantic salmon, Salmo salar L. (4/3208)

A 5.2-kb region at the 3' terminus of the salmon pancreas disease virus (SPDV) RNA genome has been cloned and sequenced. The nucleotide and predicted amino acid sequences show that SPDV shares considerable organizational and sequence identity to members of the genus alphavirus within the family Togaviridae. The SPDV structural proteins encoded by the 5.2-kb region contain a number of unique features when compared to other sequenced alphaviruses. Based on cleavage site homologies, the predicted sizes of the SPDV envelope glycoproteins E2 (438 aa) and E1 (461 aa) are larger than those of other alphaviruses, while the predicted size of the alphavirus 6K protein is 3.2 K (32 aa) in SPDV. The E2 and E1 proteins each carry one putative N-linked glycosylation site, with the site in E1 being found at a unique position. From amino acid sequence comparisons of the SPDV structural region with sequenced alphaviruses overall homology is uniform, ranging from 32 to 33%. While nucleotide sequence analysis of the 26S RNA junction region shows that SPDV is similar to other alphaviruses, analysis of the 3'-nontranslated region reveals that SPDV shows divergence in this region.  (+info)

Sequence and structural elements at the 3' terminus of bovine viral diarrhea virus genomic RNA: functional role during RNA replication. (5/3208)

Bovine viral diarrhea virus (BVDV), a member of the genus Pestivirus in the family Flaviviridae, has a positive-stranded RNA genome consisting of a single open reading frame and untranslated regions (UTRs) at the 5' and 3' ends. Computer modeling suggested the 3' UTR comprised single-stranded regions as well as stem-loop structures-features that were suspected of being essentially implicated in the viral RNA replication pathway. Employing a subgenomic BVDV RNA (DI9c) that was shown to function as an autonomous RNA replicon (S.-E. Behrens, C. W. Grassmann, H. J. Thiel, G. Meyers, and N. Tautz, J. Virol. 72:2364-2372, 1998) the goal of this study was to determine the RNA secondary structure of the 3' UTR by experimental means and to investigate the significance of defined RNA motifs for the RNA replication pathway. Enzymatic and chemical structure probing revealed mainly the conserved terminal part (termed 3'C) of the DI9c 3' UTR containing distinctive RNA motifs, i.e., a stable stem-loop, SL I, near the RNA 3' terminus and a considerably less stable stem-loop, SL II, that forms the 5' portion of 3'C. SL I and SL II are separated by a long single-stranded intervening sequence, denoted SS. The 3'-terminal four C residues of the viral RNA were confirmed to be single stranded as well. Other intramolecular interactions, e.g., with upstream DI9c RNA sequences, were not detected under the experimental conditions used. Mutagenesis of the DI9c RNA demonstrated that the SL I and SS motifs do indeed play essential roles during RNA replication. Abolition of RNA stems, which ought to maintain the overall folding of SL I, as well as substitution of certain single-stranded nucleotides located in the SS region or SL I loop region, gave rise to DI9c derivatives unable to replicate. Conversely, SL I stems comprising compensatory base exchanges turned out to support replication, but mostly to a lower degree than the original structure. Surprisingly, replacement of a number of residues, although they were previously defined as constituents of a highly conserved stretch of sequence of the SS motif, had little effect on the replication ability of DI9c. In summary, these results indicate that RNA structure as well as sequence elements harbored within the 3'C region of the BVDV 3' UTR create a common cis-acting element of the replication process. The data further point at possible interaction sites of host and/or viral proteins and thus provide valuable information for future experiments intended to identify and characterize these factors.  (+info)

In vitro infection of human peripheral blood mononuclear cells by GB virus C/Hepatitis G virus. (6/3208)

GB virus C (GBV-C), also known as hepatitis G virus, is a recently discovered flavivirus-like RNA agent with unclear pathogenic implications. To investigate whether human peripheral blood mononuclear cells (PBMC) are susceptible to in vitro GBV-C infection, we have incubated PBMC from four healthy blood donors with a human GBV-C RNA-positive serum. By means of (i) strand-specific reverse transcription-PCR, cloning, and sequencing; (ii) sucrose ultracentrifugation and RNase sensitivity assays; (iii) fluorescent in situ hybridization; and (iv) Western blot analysis, it has been demonstrated that GBV-C is able to infect in vitro cells and replicate for as long as 30 days under the conditions developed in our cell culture system. The concentration of GBV-C RNA increased during the second and third weeks of culture. The titers of the genomic strand were 10 times higher than the titers of the antigenomic strand. In addition, the same predominant GBV-C sequence was found in all PBMC cultures and in the in vivo-GBV-C-infected PBMC isolated from the donor of the inoculum. GBV-C-specific fluorescent in situ hybridization signals were confined to the cytoplasm of cells at different times during the culture period. Finally, evidence obtained by sucrose ultracentrifugation, RNase sensitivity assays, and Western blot analysis of the culture supernatants suggests that viral particles are released from in vitro-GBV-C-infected PBMC. In conclusion, our study has demonstrated, for the first time, GBV-C replication in human lymphoid cells under experimental in vitro infection conditions.  (+info)

Comparative sequence analysis of tmRNA. (7/3208)

Minimal secondary structures of the bacterial and plastid tmRNAs were derived by comparative analyses of 50 aligned tmRNA sequences. The structures include 12 helices and four pseudoknots and are refinements of earlier versions, but include only those base pairs for which there is comparative evidence. Described are the conserved and variable features of the tmRNAs from a wide phylogenetic spectrum, the structural properties specific to the bacterial subgroups and preliminary 3-dimensional models from the pseudoknotted regions.  (+info)

Attenuated virulence of pleconaril-resistant coxsackievirus B3 variants. (8/3208)

Pleconaril (VP 63843) is a novel orally bioavailable small molecule with broad antipicornavirus (enterovirus and rhinovirus) activity. Ten independently derived pleconaril-resistant variants of coxsackievirus B3 were isolated from cell culture. The molecular basis of drug resistance and the biologic properties of the drug-resistant viruses were investigated. RNA sequence analysis revealed amino acid changes in the drug-binding pocket of the resistant variants. Thermal stability studies showed the drug-resistant viruses to be significantly less stable than wild type virus. When evaluated in a murine model in which wild type virus infection is 100% lethal, the drug-resistant viruses showed attenuated virulence with both reduced mortality and delayed time to death. Virus titers in heart and spleen were dramatically lower in drug-resistant virus-infected mice than in wild type virus-infected animals. The study results indicate that pleconaril-resistant virus variants are attenuated and significantly less virulent than drug-sensitive wild type virus.  (+info)

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Stochastic Context-Free Grammars (SCFGs) were applied successfully to RNA secondary structure prediction in the early 90s, and used in combination with comparative methods in the late 90s. The set of SCFGs potentially useful for RNA secondary structure prediction is very large, but a few intuitively designed grammars have remained dominant. In this paper we investigate two automatic search techniques for effective grammars - exhaustive search for very compact grammars and an evolutionary algorithm to find larger grammars. We also examine whether grammar ambiguity is as problematic to structure prediction as has been previously suggested. These search techniques were applied to predict RNA secondary structure on a maximal data set and revealed new and interesting grammars, though none are dramatically better than classic grammars. In general, results showed that many grammars with quite different structure could have very similar predictive ability. Many ambiguous grammars were found which were at least
The development of a safe, effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades. However, despite significant progress on elucidating the function of key proteins involved in reproduction, understanding male reproductive physiology is limited by incomplete information on the genes expressed in reproductive tissues, and no contraceptive targets have so far reached clinical trials. To advance product development, further identification of novel reproductive tract-specific genes leading to potentially druggable protein targets is imperative. In this study, we expand on previous single tissue, single species studies by integrating analysis of publicly available human and mouse RNA-seq datasets whose initial published purpose was not focused on identifying male reproductive tract-specific targets. We also incorporate analysis of additional newly acquired human and mouse testis and epididymis samples to increase the number of targets identified.
Finding genes that are differentially expressed between conditions is an integral part of understanding the molecular basis of phenotypic variation. In the past decades, DNA microarrays have been used extensively to quantify the abundance of mRNA corresponding to different genes, and more recently high-throughput sequencing of cDNA (RNA-seq) has emerged as a powerful competitor. As the cost of sequencing decreases, it is conceivable that the use of RNA-seq for differential expression analysis will increase rapidly. To exploit the possibilities and address the challenges posed by this relatively new type of data, a number of software packages have been developed especially for differential expression analysis of RNA-seq data. We conducted an extensive comparison of eleven methods for differential expression analysis of RNA-seq data. All methods are freely available within the R framework and take as input a matrix of counts, i.e. the number of reads mapping to each genomic feature of interest in each of
The information contained in the genome of an organism, its DNA, is expressed through transcription of its genes to RNA, in quantities determined by many internal and external factors. As such, studying the gene expression can give valuable information for e.g. clinical diagnostics. A common analysis workflow of RNA-sequencing (RNA-seq) data consists of mapping the sequencing reads to a reference genome, followed by the transcript assembly and quantification based on these alignments. The advent of second-generation sequencing revolutionized the field by reducing the sequencing costs by 50,000-fold. Now another revolution is imminent with the third-generation sequencing platforms producing an order of magnitude higher read lengths. However, higher error rate, higher cost and lower throughput compared to the second-generation sequencing bring their own challenges. To compensate for the low throughput and high cost, hybrid approaches using both short second-generation and long third-generation ...
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Abstract] Nowadays, the analysis of transcriptome sequencing (RNA-seq) data has become the standard method for quantifying the levels of gene expression. In RNA-seq experiments, the mapping of short reads to a reference genome or transcriptome is considered a crucial step that remains as one of the most time-consuming. With the steady development of Next Generation Sequencing (NGS) technologies, unprecedented amounts of genomic data introduce significant challenges in terms of storage, processing and downstream analysis. As cost and throughput continue to improve, there is a growing need for new software solutions that minimize the impact of increasing data volume on RNA read alignment. In this work we introduce HSRA, a Big Data tool that takes advantage of the MapReduce programming model to extend the multithreading capabilities of a state-of-the-art spliced read aligner for RNA-seq data (HISAT2) to distributed memory systems such as multi-core clusters or cloud platforms. HSRA has been built ...
The rapid expansion of transcriptomics from increased affordability of next-generation sequencing (NGS) technologies generates rocketing amounts of gene expression data across biology and medicine, and notably in cancer research. Concomitantly, many bioinformatics tools were developed to streamline gene expression analysis and quantification. We tested the concordance of NGS RNA sequencing (RNA-seq) analysis outcomes between the two predominant programs for reads alignment, HISAT2 and STAR, and the two most popular programs for quantifying gene expression in NGS experiments, edgeR and DESeq2, using RNA-seq data from a series of breast cancer progression specimens, which include histologically confirmed normal, early neoplasia, ductal carcinoma in situ and infiltrating ductal carcinoma samples microdissected from formalin fixed, paraffin embedded (FFPE) breast tissue blocks. We identified significant differences in aligners’ performance: HISAT2 was prone to misalign reads to retrogene genomic loci,
Bacterial resistance to antibiotics is a growing health problem that is projected to cause more deaths than cancer by 2050. Consequently, novel antibiotics are urgently needed. Since more than half of the available antibiotics target the structurally conserved bacterial ribosomes, factors involved in protein synthesis are thus prime targets for the development of novel antibiotics. However, experimental identification of these potential antibiotic target proteins can be labor-intensive and challenging, as these proteins are likely to be poorly characterized and specific to few bacteria. Here, we use a bioinformatics approach to identify novel components of protein synthesis. In order to identify these novel proteins, we established a Large-Scale Transcriptomic Analysis Pipeline in Crowd (LSTrAP-Crowd), where 285 individuals processed 26 terabytes of RNA-sequencing data of the 17 most notorious bacterial pathogens. In total, the crowd processed 26,269 RNA-seq experiments and used the data to construct
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Purpose: Ischemia-reperfusion injury (IRI) during liver transplantation is an important factor that leads to graft dysfunction and even recipient death. This study aims to explore the effect of IRI on the transcriptome of intrahepatic cells in single cell level. *Methods: We collected tissue samples from donor liver before procurement, post-preservation and 2 hours post-reperfusion and then performed single-cell RNA, T cell receptor (TCR) and B cell receptor (BCR) sequencing. We annotated the subpopulations of intrahepatic cells and compared their changes in gene expression profiling after IRI. Combined with the bulk RNA sequencing data in our center, we explored the potential therapeutic targets of IRI. *Results: After enzymatic digestion and fluorescence activated cell sorting (FACS), 15013 cells were captured and sub-clustered into 17 subsets (Fig. 1A). We annotated each cluster and described the abundance and number of differentially expressed genes in each cluster after IRI (Fig. 1B & C). ...
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.
The recent development of sensitive protocols allows to generate RNA-seq libraries of single cells. The throughput of such scRNA-seq protocols is rapidly increasing, enabling the profiling of tens of thousands of cells and opening exciting possibilities to analyse cellular identities. In this context, unique molecular identifiers (UMIs) are used to reduce amplification noise and sample-specific ...
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Here, using single-cell RNA sequencing, we examine the stromal compartment in murine melanoma and draining lymph nodes (LNs) at points across tumor development, providing data at http://www.teichlab.org/data/. Naive lymphocytes from LNs undergo activation and clonal expansion within the tumor, befor …
Live Webinar on RNA-Seq Data Analysis Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical ...
Transcriptome analysis using RNA sequencing (RNA-seq) empowers a deeper understanding of genetics by enabling RNA expression analysis over the entire transcriptome with high sensitivity and a wide dynamic range. One powerful application within this field is stranded total RNA-seq, which makes it possible to distinguish overlapping genes and to conduct comprehensive annotation and quantification of long noncoding RNAs. Typical solutions for total RNA-seq library prep require relatively high input amounts, in the range of 100 ng to 1 µg, and it is standard practice to remove the ribosomal RNA (rRNA) from the total RNA sample prior to cDNA synthesis and library preparation. Clontech was a pioneer in the development of a low-input solution, RiboGone technology for rRNA removal from total RNA, enabling library construction from inputs spanning 10 ng to 100 ng. We integrated this technology into our SMARTer stranded RNA-seq kits, reducing the representation of rRNA in the final libraries and leading ...
Transcriptome analysis using RNA sequencing (RNA-seq) empowers a deeper understanding of genetics by enabling RNA expression analysis over the entire transcriptome with high sensitivity and a wide dynamic range. One powerful application within this field is stranded total RNA-seq, which makes it possible to distinguish overlapping genes and to conduct comprehensive annotation and quantification of long noncoding RNAs. Typical solutions for total RNA-seq library prep require relatively high input amounts, in the range of 100 ng to 1 µg, and it is standard practice to remove the ribosomal RNA (rRNA) from the total RNA sample prior to cDNA synthesis and library preparation. Clontech was a pioneer in the development of a low-input solution, RiboGone technology for rRNA removal from total RNA, enabling library construction from inputs spanning 10 ng to 100 ng. We integrated this technology into our SMARTer stranded RNA-seq kits, reducing the representation of rRNA in the final libraries and leading ...
Identification of bimodally expressed genes is an important task, since genes with bimodal expression play important roles in cell differentiation, signaling, and disease progression. Several useful algorithms have been developed to identify bimodal genes from microarray data. Currently, no method can deal with data from next generation sequencing, which is emerging as a replacement technology for microarrays. A team led by scientists at M. D. Anderson Cancer Center have developed SIBER (Systematic Identification of Bimodally Expressed genes using RNAseq data) for effectively identifying bimodally expressed genes from next generation RNAseq data. They evaluate several candidate methods for modeling RNAseq count data and compare their performance in identifying bimodal genes through both simulation and real data analysis. They show that the lognormal mixture model performs best in terms of power and robustness under various scenarios. The scientists also compare our method with alternative approaches
For example, a 3 mRNA-Seq approach generates sequencing reads localized to the 3 end of mRNAs. Therefore, it is a highly convenient method for multiplexing a large number of samples, does not require poly(A) enrichment prior to library preparation, and allows to accurately quantify gene expression with minimal computational resources. You can find short overview of read depth requirements in our blog article How many reads do I need for my RNA-Seq samples?. These features make 3 mRNA-Seq the method of choice for gene expression profiling, especially for high-throughput projects. However, due to the fact that reads are localized to the 3 ends of the transcripts, this method is not suitable to assess alternative splicing within the transcript body, investigate differential transcript usage, or for the identification of transcript isoforms. Thus, if this level of information is required, a whole transcriptome library preparation method that provides full transcript coverage would be the ...
This article will focus on conventional applications of RNA Sequencing, and will explore mining information for cSNP, Insertions Deletions & Fusion Genes, Alternate Splicing, Novel Genes/Exon, eQTL, and more. RNA Sequencing is a treasure-chest of information and quiet often we miss on potential ground breaking information in the RNA-SEQ datasets. While we normally plan an. Read More. ...
The Xenopus embryo has provided key insights into fate specification, the cell cycle, and other fundamental developmental and cellular processes, yet a comprehensive understanding of its transcriptome is lacking. Here, we used paired end RNA sequencing (RNA-seq) to explore the transcriptome of Xenopus tropicalis in 23 distinct developmental stages. We determined expression levels of all genes annotated in RefSeq and Ensembl and showed for the first time on a genome-wide scale that, despite a general state of transcriptional silence in the earliest stages of development, approximately 150 genes are transcribed prior to the midblastula transition. In addition, our splicing analysis uncovered more than 10,000 novel splice junctions at each stage and revealed that many known genes have additional unannotated isoforms. Furthermore, we used Cufflinks to reconstruct transcripts from our RNA-seq data and found that ∼13.5% of the final contigs are derived from novel transcribed regions, both within ...
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Results IgG4 was the most over-expressed mRNA in both MD and IgG4RD (fold,32; qIgG4RD=0.001, qMD=0.002), with IgE mRNA among the top 10 most over-expressed (fold,8; qIgG4RD=0.0003, qMD=0.01) and both correlated with each other (r=0.85) and IL-5R mRNA (rIgG4=0.80; rIgE=0.64), which was suppressed in patients treated with prednisone compared to those not (pIgG4RD=0.008; pMD=0.0001). The same mRNA suppression of IgG4 and IgE was seen in MD patients on prednisone compared to those not (pIgG4=0.002 and pIgG4RD=0.004; pIgG4RD=0.03; pMD=0.03).. ...
With the advancement of second generation sequencing techniques, our ability to detect and quantify RNA editing on a global scale has been vastly improved. As a result, RNA editing is now being studied under a growing number of biological conditions so that its biochemical mechanisms and functional roles can be further understood. However, a major barrier that prevents RNA editing from being a routine RNA-seq analysis, similar to gene expression and splicing analysis for example, is the lack of user-friendly and effective computational tools.|br| Based on years of experience of analyzing RNA editing using diverse RNA-seq datasets, we have developed a software tool RED-ML: RNA Editing Detection based on Machine learning (pronounced as
Rcount: simple and flexible RNA-Seq read counting. Marc W. Schmid* and Ueli Grossniklaus. Institute of Plant Biology and Zu€rich-Basel Plant Science Center, University of Zurich, 8008 Zu€rich, Switzerland. Bioinformatics. doi:10.1093/bioinformatics/btu680, PMID: 25322836. Nate showed me this paper today which is of some interest to us given my obsession with finding a better way to deal with the issue of multi-mapping reads in small RNA-seq data (e.g., with the butter program). This paper describes a tool called Rcount, which is a counter for normal mRNA-seq data. As described in the paper, Rcount takes in a BAM file, and deals with multireads. According to figure 1 (copied below), the way they do this is to use the density of local uniquely mapped reads and make a probability assessment… the more uniquely mapped reads in an area, the more likely it is that the multi-read also came from that location. They then place it, noting their calculated probability in the SAM line with a custom ...
We will explain how to start with raw data, and perform the standard processing and normalization steps to get to the point where one can investigate relevant biological questions. Throughout the case studies, we will make use of exploratory plots to get a general overview of the shape of the data and the result of the experiment. We start with RNA-seq data analysis covering basic concepts of RNA-seq and a first look at FASTQ files. We will also go over quality control of FASTQ files; aligning RNA-seq reads; visualizing alignments and move on to analyzing RNA-seq at the gene-level: counting reads in genes; Exploratory Data Analysis and variance stabilization for counts; count-based differential expression; normalization and batch effects. Finally, we cover RNA-seq at the transcript-level: inferring expression of transcripts (i.e. alternative isoforms); differential exon usage. We will learn the basic steps in analyzing DNA methylation data, including reading the raw data, normalization, and ...
The fourth data release from the NIMH SCAP-T study has been made public in the dbGaP system. This release is a revision of previously released data, and adds no new cells.. Individual-level data are now available for download by authorized investigators at http://view.ncbi.nlm.nih.gov/dbgap-controlled. These data may be browsed at the dbGaP study home page: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000833.v4.p1 dbGaP Study Release Notes. ...
DESCRIPTION. SCmut is a novel and robust statistical method for cell-level somatic mutation detection from single-cell RNA-sequencing. ...
This data set contains the raw .fastq files from two RNA-sequencing experiments and two small RNA-sequencing experiments. Both control brain tissue and tissue from sufferers of mesial temporal lobe epilepsy were sequenced. Two different brain regions were sequenced; the cortex and the hippocampus. For more details please see: Mills, James D., et al. Coding and non-coding transcriptome of mesial temporal lobe epilepsy: Critical role of small non-coding RNAs. Neurobiology of disease 134 (2020): 104612 ...
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Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in humans. Human transcript sequences from the International Nucleotide Sequence Database ...
RNA sequencing reveals the differences between chemical and chronic constipation induction of intestinal tumor, Yunpeng Luan, Yong Cao, Dechang Mao, Yanmei Li, Xiaoguang Yue, Youji
PhD Project - Mitochondrial Genomics: Computational analysis of RNA sequencing data to unravel post-transcriptional processes influencing mitochondrial function at Kings College London, listed on FindAPhD.com
Manduca sexta is a large lepidopteran insect widely used as a model to study biochemistry of insect physiological processes. As a part of its genome project, over 50 cDNA libraries have been analyzed to profile gene expression in different tissues and life stages. While the RNA-seq data were used to study genes related to cuticle structure, chitin metabolism and immunity, a vast amount of the information has not yet been mined for understanding the basic molecular biology of this model insect. In fact, the basic features of these data, such as composition of the RNA-seq reads and lists of library-correlated genes, are unclear. From an extended view of all insects, clear-cut tempospatial expression data are rarely seen in the largest group of animals including Drosophila and mosquitoes, mainly due to their small sizes. We obtained the transcriptome data, analyzed the raw reads in relation to the assembled genome, and generated heatmaps for clustered genes. Library
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From the Department of Developmental Biology (K.-C.Y., J.M.N.) and Center for Cardiovascular Research, Division of Cardiology, Department of Internal Medicine (K.A.Y., A.Y.P., V.K.T., G.A.E., D.L.M.), Washington University Medical School, St. Louis, MO; Division of Cardiothoracic Surgery, New York Presbyterian Hospital, Columbia University College of Physicians and Surgeons, New York, NY (I.G.); and Department of Surgery, University of Maryland School of Medicine, Baltimore (F.H.C.). Dr Yangs current affiliation is the Department of Pharmacology, National Taiwan University School of Medicine, Taipei, Taiwan. ...
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Massively parallel cDNA sequencing (RNA-seq) experiments are gradually superseding microarrays in quantitative gene expression profiling. However, many biologists are uncertain about the choice of differentially expressed gene (DEG) analysis methods and the validity of cost-saving sample pooling strategies for their RNA-seq experiments. Hence, we performed experimental validation of DEGs identified by Cuffdiff2, edgeR, DESeq2 and Two-stage Poisson Model (TSPM) in a RNA-seq experiment involving mice amygdalae micro-punches, using high-throughput qPCR on independent biological replicate samples. Moreover, we sequenced RNA-pools and compared their results with sequencing corresponding individual RNA samples. False-positivity rate of Cuffdiff2 and false-negativity rates of DESeq2 and TSPM were high. Among the four investigated DEG analysis methods, sensitivity and specificity of edgeR was relatively high. We documented the pooling bias and that the DEGs identified in pooled samples suffered low positive
Covaris Adaptive Focused Acoustics® (AFA®) has long been the gold standard for unbiased, efficient, and highly reproducible shearing of DNA for NGS library preparation workflows. The same technology is also available for an unbiased, efficient, and highly reproducible shearing of total RNA, mRNA, and cDNA for RNA-Seq library preparation.. RNA sequencing applications using NGS have been the technique of choice for carrying out whole transcriptome sequencing, monitoring gene expression, and elucidating products of gene splicing and post transcriptional modifications. The recent implication of gene fusion events in tumorigenesis and their potential utility in diagnostics enables a higher level of tumor classification. In drug discovery, it specifically targets products of gene fusion events. This combination brings new focus on the use of RNA-Seq in the clinic for tumor classification, cancer progression, and treatment monitoring.. Chemical fragmentation of RNA is highly sensitive to sample ...
PubMed Central Canada (PMC Canada) provides free access to a stable and permanent online digital archive of full-text, peer-reviewed health and life sciences research publications. It builds on PubMed Central (PMC), the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature and is a member of the broader PMC International (PMCI) network of e-repositories.
Replication Data for publication: Enterococcus faecalis adapts to antimicrobial conjugated oligoelectrolytes by lipid rearrangement and differential expression of membrane stress response genes. Includes: RNA sequencing data: RAW reads RNA sequencing data: non rRNA reads RNA sequencing data: extracted counts See RNAseq-readme.txt for file description.
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PubMed Central Canada (PMC Canada) provides free access to a stable and permanent online digital archive of full-text, peer-reviewed health and life sciences research publications. It builds on PubMed Central (PMC), the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature and is a member of the broader PMC International (PMCI) network of e-repositories.
BACKGROUND: Renal endothelial cells from glomerular, cortical, and medullary kidney compartments are exposed to different microenvironmental conditions and support specific kidney processes. However, the heterogeneous phenotypes of these cells remain incompletely inventoried. Osmotic homeostasis is vitally important for regulating cell volume and function, and in mammals, osmotic equilibrium is regulated through the countercurrent system in the renal medulla, where water exchange through endothelium occurs against an osmotic pressure gradient. Dehydration exposes medullary renal endothelial cells to extreme hyperosmolarity, and how these cells adapt to and survive in this hypertonic milieu is unknown.. METHODS: We inventoried renal endothelial cell heterogeneity by single-cell RNA sequencing ,40,000 mouse renal endothelial cells, and studied transcriptome changes during osmotic adaptation upon water deprivation. We validated our findings by immunostaining and functionally by targeting oxidative ...
TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/ .
Bioconductor version: Release (3.13) Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model is by far the most frequently adopted. However, common methods that are based on a negative binomial model are not robust to extreme outliers, which we found to be abundant in public datasets. So far, no rigorous and probabilistic methods for detection of outliers have been developed for RNA sequencing data, leaving the identification mostly to visual inspection. Recent advances in Bayesian computation allow large-scale comparison of observed data against its theoretical distribution given in a statistical model. Here we propose ppcseq, a key quality-control tool for identifying transcripts that include outlier data points in differential expression analysis, which do not follow a negative binomial distribution. Applying ppcseq ...
Cancer WTS service in Creative Biolabs enable discovery and profiling of RNAs in any species without prior genome annotation. Our seasoned scientists provide the most accurate detection and quantification of rare RNA sequences and sequence variants.
IEEE Xplore, delivering full text access to the worlds highest quality technical literature in engineering and technology. | IEEE Xplore
Detailed analysis of two brain tumor subtypes by investigators at Massachusetts General Hospital and the Broad Institute of MIT and Harvard has revealed that they may originate from the same type of neural progenitor cells and be distinguished by gene mutation patterns and by the composition of their microenvironments.
Deep sequencing analysis of gene expression (DSAGE) measures global gene transcript levels from only 1 to 2 µg total RNA by massively parallel sequencing of cDNA tags
The SePIA workflow allows analysis of paired-end total RNA, poly(A)-derived RNA, and single-end small RNA data. All three data types were processed by the same RNA-seq components at common steps in the workflow, such as preprocessing and alignment, to produce standardized outputs. The ease in which SePIAs pipelines can be extended was demonstrated in Case I, where variant calling was performed as an additional, independently-executed analysis of transcript-level data. Integrated analysis was demonstrated in Case II, identifying biologically interesting miRNA-mRNA pairs by combining expression correlation with in silico target predictions [24]. Though Cufflinks and HTSeq are used in the workflow for mapped read quantification, users may prefer other tools such as RSEM [50], eXpress [51], and BitSeq [52]. These are available as components that can also be used with SePIA and instructions on how to implement them is given on the SePIA website. Users with a basic proficiency in a programming ...
1 were set as the cut‑off criteria to screen for differentially expressed genes (DEGs). Differential gene co‑expression analysis was performed using R/EBcoexpress package in R. DEGs in the gene co‑expression network were subjected to Gene Ontology analysis using the Database for Annotation, Visualization and Integration Discovery. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was also performed on the DEGs using KOBAS 2.0 software. The ConnectivityMap database was used to identify novel drug candidates. A total of 3,742 DEGs were identified among the 552 UCEC samples and 35 normal controls, and comprised 2,580 upregulated and 1,162 downregulated genes. A gene co‑expression network consisting of 129 DEGs and 368 edges was constructed. Genes were associated with the cell cycle and the tumor protein p53 signaling pathway. Three modules were identified, in which genes were associated with the mitotic cell cycle, nuclear division and the M phase of the mitotic cell ...
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. https://edrn.jpl.nasa.gov/publications/21724842-deep-sequencing-reveals-distinct-patterns https://edrn.jpl.nasa.gov/logo.png ...
These scripts assess differential expression between monogamous and non-monogamous species between all clades and across evolutionary subgroupings. Different approaches to differential expression analysis were used to identify novel candidates associated with monogamy. --RRHO.html: R script that performs the Rank Rank Hypergeometric Overlap (RRHO) between all pairwise clades, generates lists of most up- and down-regulated OGGs, and generates the RRHO and summary plots --DESeq2_volcanoplots.html: R script that performs DESeq2 of different evolutionary subgroups and generates volcano plots. --NovelCandidates.html: Integrate Log2 fold difference, DESeq2 all vertebrates, and RRHO most up- and down-regulated genes to generate a heatmap of novel candidates
Transcription Support Level (TSL): It is important that users understand how to assess transcript annotations that they see in GENCODE. While some transcript models have a high level of support through the full length of their exon structure, there are also transcripts that are poorly supported and that should be considered speculative. The Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.. The mRNA and EST alignments are compared to the GENCODE transcripts and the transcripts are scored according to how well the alignment matches over its full length. The GENCODE TSL provides a consistent method of evaluating the level of support that a GENCODE transcript annotation is actually expressed in mouse. Mouse transcript sequences from the International Nucleotide Sequence Database ...
I am working on analysis for an RNASeq experiment with the end goal of using DESeq2 to generate a list of differentially expressed genes. We have 4 biological replicates for 4 conditions (differing genotypes in mice). We have 50 bp single ended Illumina read sets, on total RNA (they had low input and needed to go with an UltraLow kit thus the total RNA rather than say pA selected/RiboZero).. I have run Salmon on the fastq files using a mouse GRCm38 v3 cDNA all fasta file as the source to build a Salmon index file, and have read counts at transcript level for every data set. We have compared this at first glance to a prior dataset from a similar prior experiment (I dont know much about the analysis for this prior exit) and the top expressed genes by count show anticipated overlap- literally just looking by eye) so things superficially seem to be heading in the right direction.. Here is the meat of the question, the manual for DESeq(2) is quite clear that they require raw counts as input, and ...
The identification and molecular characterization of cellular hierarchies in complex tissues is key to understanding both normal cellular homeostasis and tumorigenesis. The mammary epithelium is a heterogeneous tissue consisting of two main cellular compartments, an outer basal layer containing myoepithelial cells and an inner luminal layer consisting of estrogen receptor-negative (ER−) ductal cells and secretory alveolar cells (in the fully functional differentiated tissue) and hormone-responsive estrogen receptor-positive (ER+) cells. Recent publications have used single-cell RNA-sequencing (scRNA-seq) analysis to decipher epithelial cell differentiation hierarchies in human and murine mammary glands, and reported the identification of new cell types and states based on the expression of the luminal progenitor cell marker KIT (c-Kit). These studies allow for comprehensive and unbiased analysis of the different cell types that constitute a heterogeneous tissue. Here we discuss scRNA-seq studies
Pears (Pyrus spp. L.) are an important genus of trees that produce one of the worlds oldest fruit crops. Salinity stress is a common limiting factor for plant productivity that significantly affects the flavor and nutritional quality of pear fruits. Much research has shown that calcium signaling pathways, mediated by Calcineurin B-like proteins (CBLs) and their interacting kinases (CIPKs), are closely associated with responses to stresses, including salt. However, little is known about the molecular mechanisms that govern the relationship between salt stress and calcium signaling pathways in pear plants. The available genomic information for pears has promoted much functional genomic analysis and molecular breeding of the genus. This provided an ample foundation for characterizing the transcriptome of pear under salt stress. A high-throughput Illumina RNA-seq technology was used to identify a total of 78,695 unigenes that were successfully annotated by BLASTX analysis, using the publicly available
View detailed Table of Content here - https://www.marketsandmarkets.com/Market-Reports/ngs-based-rna-seq-market-102977816.html The expression profiling analysis segment accounted for the largest share of the NGS-based RNA-sequencing market, by application, in 2018. Based on application, the NGS-based RNA sequencing market is segmented into expression profiling analysis, small RNA sequencing, De Novo transcriptome assembly, and variant calling & transcriptome epigenetics. In 2018, the expression profiling analysis segment accounted for the largest share of the NGS-based RNA sequencing market. The dominant market position of this segment is attributed mainly to the increasing prevalence of metabolic disorders, multiple sclerosis, and other diseases. These factors will continue to propel the demand for expression profiling analysis to provide specific treatment options in the market during the forecast period.. The nanopore segment is expected to register the highest growth in the NGS-based ...
Quantification of miRNA expression can be performed using a variety of technologies, including NGS and real-time PCR (qPCR). While NGS is the default tool for novel miRNA discovery, commercially available library preparation kits introduce biases and involve tedious procedures. As a result, qPCR has been the most commonly used technology for quantification of miRNA expression - until now. The QIAseq miRNA Library Kit defines a new generation in small RNA sequencing products and includes several distinct features not found in other sequencing kits. With the QIAseq miRNA Library Kit, the power of NGS has been combined with single molecule quantification from Unique Molecular Indices (UMI) to generate the most representative expression data possible. In recent years, NGS has emerged as a highly advanced research tool for both high-throughput miRNA expression analysis and novel miRNA discovery. The QIAseq miRNA Library Kit procedure does not require gel purification, excision and elution, which ...
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doi:10.1261/rna.1200508. PMC 2590952. PMID 18945806. Magnus Manske on Twitter Alastair Kerr (21 June 2011). "Desktop Sequence ... 2012). "Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing". Nature. 487 (7407): 375-9. ... "The RNA WikiProject: Community annotation of RNA families". RNA. 14 (12): 2462-2464. ... Manske, H. M.; Kwiatkowski, D. P. (2009). "Look Seq: A browser-based viewer for deep sequencing data". Genome Research. 19 (11 ...
"RNA-sequencing analysis - Clinical Lab Products". Clinical Lab Products. Retrieved 11 September 2018. BBC: Read about how ... The program is compatible with a range of Omics data, for example: RNA-seq, DNA-seq, mRNA expression, NGS, Single cell RNA-seq ... "Do it yourself and get your analysis in an instant! , Qlucore". qlucore.com. Retrieved 11 September 2018. "Publications and ... in order to address the vast amount of high-dimensional data generated with microarray gene expression analysis. As a result, ...
Eddy S. R. & Durbin R. (1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079-2088. doi ... Rivas E.; Eddy S. R. (2001). "Noncoding RNA Gene Detection Using Comparative Sequence Analysis". BMC Bioinformatics. 2 (1): 8. ... The RNA analysis package Infernal uses such profiles in inference of RNA alignments. The Rfam database also uses CMs in ... Since RNAs preserve their structures over their primary sequence; RNA structure prediction can be guided by combining ...
2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. doi:10.1038/414865a. ... 2002). "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis". RNA. 8 (4 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... RNA-binding protein Raly is a protein that in humans is encoded by the RALY gene. In infectious mononucleosis, anti-EBNA-1 ...
"Exome-based analysis for RNA epigenome sequencing data". Bioinformatics. 29 (12): 1565-1567. doi:10.1093/bioinformatics/btt171 ... DNA Sequencing. References[edit]. *^ Valouev A, et al. (September 2008). "Genome-wide analysis of transcription factor binding ... Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq[5] or m6Aseq[6] for ... It is also possible to do more complex analysis using such tools like combining multiple ChIP-seq signal to detect regulatory ...
January 2002). "Sequence analysis of measles virus nucleocapsid transcripts in patients with Paget's disease". J. Bone Miner. ... Baslé MF, Fournier JG, Rozenblatt S, Rebel A, Bouteille M (May 1986). "Measles virus RNA detected in Paget disease bone tissue ... April 2007). "Multicenter blinded analysis of RT-PCR detection methods for paramyxoviruses in relation to Paget disease of bone ... and in situ-RT-PCR for the detection of canine distemper virus RNA in Paget disease". J. Virol. Methods. 109 (2): 253-9. doi: ...
14 (12): 2462-4. doi:10.1261/rna.1200508. PMC 2590952. PMID 18945806. Eddy SR, Durbin R (June 1994). "RNA sequence analysis ... October 2008). "The RNA WikiProject: Community annotation of RNA families". RNA. ... Eddy SR (2002). "A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary ... Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an ...
Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986). "The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences". In ... In contrast, sequence-driven analysis uses conserved DNA sequences to design PCR primers to screen clones for the sequence of ... sequences many short sequences, and reconstructs them into a consensus sequence. Shotgun sequencing reveals genes present in ... "Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses". Proceedings of the National Academy of Sciences ...
Bacher, Rhonda; Kendziorski, Christina (2016-04-07). "Design and computational analysis of single-cell RNA-sequencing ... A collection of 50+ trajectory inference methods within a common interface A table of tools for the analysis of single-cell RNA ... Ji, Zhicheng; Ji, Hongkai (2016-05-13). "TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis". ... Hwang, Byungjin; Lee, Ji Hyun; Bang, Duhee (2018-08-07). "Single-cell RNA sequencing technologies and bioinformatics pipelines ...
"High-Resolution Genomic Analysis of Human Mitochondrial RNA Sequence Variation". Science. 344 (6182): 413-415. doi:10.1126/ ... including the analysis and functional analysis groups of the 1000 Genomes Project and the Pan Cancer Analysis of Whole Genomes ... Other discoveries include large scale RNA methylation and its genetic control in human mitochondria and the impact of ... "Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans ...
"In situ sequencing for RNA analysis in preserved tissue and cells". Nature Methods. 10 (9): 857-860. doi:10.1038/nmeth.2563. ... in situ RNA sequencing[3], DNA sequencing, antibody based immunofluorescence tissue assays, molecular profiling of pathogens, ... and analysis of bacterial genes for antimicrobial resistance.[2] Integration of "molecular pathology" and "epidemiology" led to ...
... is a long non-coding RNA. In humans, it is located on the X chromosome. It was identified during sequence analysis of the X ... 2002). "Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine". Genome Res. 12 (6): 894 ... Long noncoding RNA "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine ... 2011). "Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region ...
... and sequencing by ligation techniques. It allows spatial transcriptome analysis in fixed cells. RNA is first reverse ... Captured RNA is amplified and sequenced. Transcript localization is determined by the barcode oligonucleotide sequence from the ... This method allows further RNA transcript profiling and cDNA library generation of the retrieved cells. RNA sequencing of the ... An advanced alternative for RNA Sequencing of Individual Cryosections described above, RNA tomography (tomo-seq) features ...
Cloning and sequence analysis of the complementary DNA". Biochemistry. 26 (13): 3975-82. doi:10.1021/bi00387a035. PMID 3651428 ... Misrahi M, Atger M, Milgrom E (1987). "A novel progesterone-induced messenger RNA in rabbit and human endometria. ...
a b Wolf, P. G. (1995). "Phylogenetic Analyses of rbcL and Nuclear Ribosomal RNA Gene Sequences in Dennstaedtiaceae." American ... Wolf, P. G. (1997). "Evaluation of atpB Nucleotide Sequences for Phylogenetic Studies of Ferns and Other Pteridophytes." ... 1995). "Fern Phylogeny Based on rbcL Nucleotide Sequences." American Fern Journal 85(4): 134-181 ...
... a web-based RNA alignment tool; WebMGA, a customizable web server for fast metagenomic sequence analysis; and DNACLUST, a tool ... Wu S, Zhu Z, Fu L, Niu B, Li W (September 2011). "WebMGA: a customizable web server for fast metagenomic sequence analysis". ... The project also financed deep sequencing of bacterial 16S rRNA sequences amplified by polymerase chain reaction from human ... Study methods included 16S rRNA gene profiling, whole metagenome shotgun sequencing, whole genome sequencing, ...
The 5' end is about 80 nucleotides in length and typically begins with the sequence GAAAA. In addition to its RNA polymerase ... "Sequence analysis of 43‐year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X ... the RNA dependent RNA polymerase, three proteins - the triple gene block (TGB) 1, 2 and 3 - and the coat protein. The RNA is ... This in turn produces a negative stranded template from which a series of subgenomic RNAs are generated. These subgenomic RNAs ...
A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing. in: RNA vol. 6,2 pg. ... Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. in: Proc. Natl. Acad. Sci. U.S. ... Liu QJ, Gong YQ, Chen BX, et al.: [Linkage analysis and mutation detection of GRIA3 in Smith--Fineman--Myers syndrome] in: Yi ... Rampersad V, Elliott CE, Nutt SL, et al.: Human glutamate receptor hGluR3 flip and flop isoforms: cloning and sequencing of the ...
March 2007). "Suitability of partial 16S ribosomal RNA gene sequence analysis for the identification of dangerous bacterial ... "Identification of Burkholderia pseudomallei and related bacteria by multiple-locus sequence typing-derived PCR and real-time ...
MiRNAs are formed from longer sequences of RNA that are cut free by a Dicer enzyme from an RNA sequence that is from a ... This also allows for analysis, like comparing the sequences of two different species. Shorthands have been developed for ... And three is by providing a new double-stranded RNA (dsRNA) sequence that Dicer can act upon to create more miRNA to find and ... Self-complementarity refers to the fact that a sequence of DNA or RNA may fold back on itself, creating a double-strand like ...
Analyses of the genome sequences resulted in the discovery of a conserved RNA motif. Heckmann, K. and H. J. Schmidt (1987) ...
"Organisation and sequence analysis of nuclear-encoded 5s ribosomal RNA genes in cryptomonad algae". Curr. Genet. 27 (3): 239-42 ...
"A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing". RNA. 6 (2): 257-69. ... The editing complementary sequence (ECS) is found in an intronic sequence close to the exon. The intronic sequence includes a 5 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... GluR3 is a gene product of the GRIA3 gene and its pre-mRNA is subject to RNA editing. A to I RNA editing is catalyzed by a ...
The researchers used sequence analysis and quantitative genomics assays on HHV DNA. In the U. Florida study, the LAT region was ... The LAT RNA is produced by genetic transcription from a certain region of the viral DNA. LAT regulates the viral genome and ... In 1991, Farrell and colleagues reported that the 2.0-kb LAT intron terminates at the 5′ end with a 750-base antisense RNA ... Further research has shown that HHV-8 LAT produces RNA which interfere not with expression of TGF-β1 and SMAD3, but reducing ...
2002). "Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine". Genome Res. 12 (6): 894 ... PMID 12045143.CS1 maint: DOI inactive as of January 2021 (link) Tian D, Sun S, Lee JT (2010). "The long noncoding RNA, Jpx, is ... 2002). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... It was identified during sequence analysis of the X inactivation centre, surrounding the Xist gene. Jpx upregulates expression ...
"Organisation and sequence analysis of nuclear-encoded 5s ribosomal RNA genes in cryptomonad algae". Current Genetics. 27 (3): ...
"A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing". RNA. 6 (2): 257-69. ... "Intron sequence directs RNA editing of the glutamate receptor subunit GluR2 coding sequence". Proc. Natl. Acad. Sci. U.S.A. 91 ... The type of RNA editing that occurs in the pre-mRNA of GluR-2 is Adenosine-to-Inosine (A-to-I) editing. [11] A-to-I RNA editing ... A-to-I editing occurs in a non coding RNA sequences such as introns, untranslated regions (UTRs), LINEs, SINEs (especially Alu ...
Kozak M (October 1987). "An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs". Nucleic Acids Research. 15 ... Sequence covariation methods rely on the existence of a data set composed of multiple homologous RNA sequences with related but ... Teunissen, A. W. M. (1979). RNA Structure Probing: Biochemical structure analysis of autoimmune-related RNA molecules. pp. 1-27 ... the Shine-Dalgarno sequence, the Kozak consensus sequence and the RNA polymerase III terminator. The secondary structure is the ...
Kozak, M (October 1987). "An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs". Nucleic Acids Res. 15 (20 ... Kozak, M (26 October 1987). "An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs". Nucleic Acids Research ... Her most cited work was from 1984, entitled "Compilation and analysis of sequences upstream from the translational start site ... Kozak, M. (1991-11-15). "An analysis of vertebrate mRNA sequences: intimations of translational control". The Journal of Cell ...
The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human ... 除了蛋白質編碼基因之外,人類的基因組還包含了數千個RNA基因(製造非編碼RNA),其中包括用來轉錄轉運RNA(tRNA)、核糖體RNA(rRNA)與信使RNA(mRNA)的基因。其中轉錄rRNA的基因稱為rDNA,分佈在許多不同的染色體上。 ... International Human Genome Sequencing Consortium. Initial sequencing
RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ... negative regulation of transcription from RNA polymerase II promoter. • positive regulation of transcription from RNA ...
"Ingenuity IPA Software - Pathway Analysis, miRNA, NGS, RNA-Seq, Microarrays, Gene Expression, Biomarkers". Ingenuity Systems. ... Laboratory Corporation and Quest Diagnostics to develop a solution for scoring genetic variation for next generation sequencing ... "The Return on Investment for Ingenuity Pathways Analysis within the Pharmaceutical Value Chain", Zimmerman, Reeve, and Golden, ... "Ingenuity Preps New NGS Variant Analysis Tool, Signs Translational Oncology Group as Beta Tester". BioInform. GenomeWeb. ...
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December 1999). "Identification of Ebola virus sequences present as RNA or DNA in organs of terrestrial small mammals of the ... an analysis of Ebola virus RNA results and behavioural data". Lancet Global Health. 4 (10): e736-e743. doi:10.1016/S2214-109X( ... of bats were found to contain both RNA sequences and IgG molecules indicating Ebola infection.[87] Antibodies against Zaire and ... Finding the virus, viral RNA, or antibodies in blood[1]. Differential diagnosis. Malaria, cholera, typhoid fever, meningitis, ...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-45. doi:10.1038/ ... RNA expression pattern. More reference expression data. Gene ontology. Molecular function. • ion channel activity. • ...
3.4 RNA editing in plastids. *4 Protein targeting and import *4.1 Cytoplasmic translation and N-terminal transit sequences ... "Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of ... RNA editing in plastidsEdit. RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior ... Its existence was first proven in 1962,[4] and first sequenced in 1986-when two Japanese research teams sequenced the ...
... es and other coleoid cephalopods are capable of greater RNA editing (which involves changes to the nucleic acid sequence ... implied alignment and analysis methods". Journal of Molluscan Studies. 73 (4): 399-410. doi:10.1093/mollus/eym038.. ... Coleoids rely mostly on ADAR enzymes for RNA editing, which requires large double-stranded RNA structures to flank to the ... High levels of RNA editing do not appear to be present in more basal cephalopods or other molluscs.[118][119] ...
RNA polymerase II core promoter sequence-specific DNA binding. • RNA polymerase II transcription factor activity, sequence- ... "A comprehensive analysis of PAX8 expression in human epithelial tumors". The American Journal of Surgical Pathology. 35 (6): ... transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding. • RNA polymerase ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. ...
... gene with an imperfect polyadenylation signal sequence". The Journal of Clinical Investigation. 99 (3): 520-5. PMC 507827. . ... characterization and expression analysis of the human septin SEPT8 (KIAA0202)". Gene. 312: 313-20. PMID 12909369. doi:10.1016/ ...
RNA probes can be designed for any gene or any sequence within a gene for visualization of mRNA,[3][4][5] lncRNA[6][7][8] and ... In the eventual analysis, these fragments were put into order by digesting a copy of each fragment into still smaller fragments ... Single-molecule RNA FISH[edit]. Single-molecule RNA FISH, also known as Stellaris® RNA FISH,[11] is a method of detecting and ... In biology, a probe is a single strand of DNA or RNA that is complementary to a nucleotide sequence of interest. ...
Sarkisian CJ, Master SR, Huber LJ, Ha SI, Chodosh LA (Oct 2001). "Analysis of murine Brca2 reveals conservation of protein- ... RAD51 catalyses strand transfer between a broken sequence and its undamaged homologue to allow re-synthesis of the damaged ... messenger RNA. [13]. Breast cancer (progesteron receptor negative). Over-expression. -. messenger RNA. [16]. ... They each share about 25% amino acid sequence identity with RAD51 and with each other.[28] ...
Sunseeker International is a main motor yacht manufacturer; it made the boat in the opening sequence of The World Is Not Enough ... "Local Authority & County Analysis 2006-2010". GBTS England LA & County & Towns 2006-2010. VisitEngland. September 2011. p. 5. ... Fourth Element (wet suits) are on the A3083 at Cury, south of RNAS Culdrose and Helston. A.P. Valves make diving equipment in ... The South West Observatory's Economy Module provides a detailed analysis of the region's economy.[129] ...
Gu C, Zeng T, Li Y, Xu Z, Mo Z, Zheng C (October 2009). "Structure-function analysis of mutant RNA-dependent RNA polymerase ... J Virol 79(21):13385-13398 Wang X, Zhang J, Lu J, Yi F, Liu C, Hu Y. Sequence analysis and genomic organization of a new insect ... strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral RDRP (RNA-Dependent RNA ... The mRNA encodes RNA dependent RNA polymerase. This polymerase makes complementary minus strands of RNA, then uses them as ...
The particular RNA molecule sequenced, known as 16s rRNA, is present in all organisms and always has the same vital function: ... Lake JA (January 1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature. 331 ... Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the ... 1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature. 331 (6152): 184-6. ...
2004). "The sequence and analysis of duplication-rich human chromosome 16". Nature. 432 (7020): 988-94. doi:10.1038/nature03187 ... SNORD71: encoding protein Small nucleolar RNA, C/D box 71. *SPSB3: encoding protein SplA/ryanodine receptor domain and SOCS box ... LINC00273 encoding protein Long intergenic non-protein coding RNA 273. *LOC124220: encoding protein Zymogen granule protein 16 ... the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number ...
... although some in vitro studies have demonstrated that RNA polymerase III can recognize TATA sequences.[25] ... "Functional analysis of the molecular interactions of TATA box-containing genes and essential genes". PLOS ONE. 10 (3): ... This sequence was originally called Box A, which is now known to be the sequence that interacts with the homologue of the ... In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" ...
... where it is initiated by recruitment of the RNA-induced transcriptional silencing (RITS) complex to double stranded RNAs ... Analysis of histone modifications in embryonic stem cells (and other stem cells) revealed many gene promoters carrying both ... 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone". The Journal of ... "Huang R C & Bonner J. Histone, a suppressor of chromosomal RNA synthesis. Proc. Nat. Acad. Sci. US 48:1216-22, 1962" (PDF). ...
"Analysis of the effect of natural sequence variation in Tat and in cyclin T on the formation and RNA binding properties of Tat- ... Michels AA, Nguyen VT, Fraldi A, Labas V, Edwards M, Bonnet F, Lania L, Bensaude O (2003). "MAQ1 and 7SK RNA interact with CDK9 ... Nguyen VT, Kiss T, Michels AA, Bensaude O (2001). "7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T ... and mitochondrial DNA sequence elements from cultured mouse and human fibroblasts". DNA Cell Biol. 20 (9): 531-54. doi:10.1089/ ...
Further analysis showed that PRK2, a direct target of Rho, is required for the formation of apical junctions. Mutational ... Further DNA testing showed that the transforming sequences in the two cancer cell lines were the same, and the gene was later ... evidence of the importance of Ral was provided when cortical neurons were depleted of endogenous RalA and RalB isoforms by RNA ... After size fractionation of FCS and analysis of the lipids that bound to serum albumin, the lysophosphatidic acid (LPA) was ...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... RNA binding. • acetyl-CoA C-acyltransferase activity. • long-chain-enoyl-CoA hydratase activity. ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... The encoded protein can also bind RNA and decreases the stability of some mRNAs. The genes of the alpha and beta subunits of ...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... positive regulation of transcription from RNA polymerase II promoter. • negative regulation of cell proliferation. • signal ... sequencing and analysis of 500 novel complete protein coding human cDNAs". Genome Res. 11 (3): 422-35. doi:10.1101/gr.GR1547R. ... 2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. doi:10.1038/ ...
Analysis of the JCVM variant revealed archetype-like regulatory regions with no mutations in coding sequences. The precise ... RNA virus. CBV. HAV (A). HCV (C). HDV (D). HEV (E). HGV (G). ... RNA virus. *IV: SARS coronavirus *Severe acute respiratory ... RNA virus. HCV Hepatocellular carcinoma. Splenic marginal zone lymphoma. HTLV-I Adult T-cell leukemia/lymphoma. ... RNA virus. MeV Subacute sclerosing panencephalitis. LCV Lymphocytic choriomeningitis. Arbovirus encephalitis. Orthomyxoviridae ...
"for his pioneering analyses of saving and of financial markets"[۱۳۸] ۱۹۸۷ رابرت سولو[۱] United States "for his contributions to ... "for their discovery of catalytic properties of RNA"[۳۳] ۱۹۹۲ رادولف مارکوس[۱] United States "for his contributions to the ... "for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active ... "for his analyses of markets with asymmetric information"[۱۴۴] ۲۰۰۲ دانیل کاهنمن[۱] Israel. United States "for having integrated ...
All modern ideas start with the sequence analysis of DNA and RNA. In 1987, Carl Woese, the forerunner of the molecular ... The complete DNA sequence is known for many bacterial strains.. Shape[change , change source]. Bacteria vary widely in size and ... phylogeny revolution, divided bacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences:[5][6] ...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... Chand A, Clark J, Cooper CS, Craig IW (1997). "Long-range organization of reiterated sequences, including the SSX1 cDNA at the ... RNA expression pattern. More reference expression data. Gene ontology. Molecular function. • protein binding. • transcription ... "The DNA sequence of the human X chromosome". Nature. 434 (7031): 325-37. doi:10.1038/nature03440. PMC 2665286 . PMID 15772651 ...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... 2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. Bibcode: ... RNA expression pattern. More reference expression data. Gene ontology. Molecular function. • cyclin-dependent protein kinase 5 ...
Schmidt TM, Relman DA (1994). Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods in ... "Identification of species by multiplex analysis of variable-length sequences". Nucleic Acids Research 38 (22): e203. PMC ... SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. ... Coenye T, Vandamme P (November 2003). "Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced ...
RNA) - ribosome - RNA - route of administration - RT-PCR - RTI - Ryan White C.A.R.E. act ... sputum analysis - standard of care - staphylococcus - STD - stem cells (FDCs) - steroid - Stevens-Johnson syndrome - STI - ... long terminal repeat sequence (LTR) - long-term nonprogressors - LTR - lumbar - lumbar puncture - lymph - lymph nodes - ... messenger RNA - metabolism - metastasis - MHC - microbes - microbicide - Microsporidiosis - mitochondria - mitochondrial ...
Specific amino acid sequences (PTS or peroxisomal targeting signal) at the C-terminus (PTS1) or N-terminus (PTS2) of ... Two independent evolutionary analyses of the peroxisomal proteome found homologies between the peroxisomal import machinery and ... The protein receptors, the peroxins PEX5 and PEX7, accompany their cargoes (containing a PTS1 or a PTS2 amino acid sequence, ...
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses Message Subject (Your Name) has sent you a message ...
... by following key player positioning and monitoring the top competitors ... RNA Sequencing: Technologies and Analyses of Global Market Trends "The Latest Research Report RNA Sequencing: Technologies and ... consumables for RNA sequencing; RNA sequencing services; and data analysis, storage, and management. Sample preparation is ... Exhaustive analysis of the RNA sequencing market by type helps to understand the types of sequencing technologies that are ...
Only on a single-cell level, can you eliminate the biological noise that is inherent to standard gene expression analysis - ... Get more powerful data from single cells - detect more transcripts with the same sequencing depth, including both mRNA and ... Our new solutions for single-cell RNA-seq deliver a deeper understanding of the transcriptome, providing new biological ... lncRNA, providing deeper insights into the transcriptome and unveiling the expression of important regulatory RNAs. ...
... we developed a method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and ... In alternative expression analysis by sequencing (ALEXA-seq), ... Alternative expression analysis by RNA sequencing Nat Methods. ... In alternative expression analysis by sequencing (ALEXA-seq), we developed a method to analyze massively parallel RNA sequence ... Alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis are ...
In situ sequencing for RNA analysis in preserved tissue and cells.. Ke R1, Mignardi M, Pacureanu A, Svedlund J, Botling J, ... We have developed an in situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically ... We demonstrate in situ sequencing of point mutations and multiplexed gene expression profiling in human breast cancer tissue ...
Analysis and design of RNA sequencing experiments for identifying isoform regulation.. Katz Y1, Wang ET, Airoldi EM, Burge CB. ... analysis in human cells. Our results provide a probabilistic framework for RNA-seq analysis, give functional insights into pre- ... Bayes factor analysis of hnRNP H regulation of exon splicing. (a) CLIP tag density (H CLIP; green) and RNA-seq read densities ... To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms ( ...
... fundamental modifications to RRM had to be made in order to make it suitable for the analysis of a greater variety of sequences ... During the course of the project, several methods for extracting the features from the spectra of biological sequences and ... For promoter classification the suitable choices were found to be Principal Component Analysis (PCA) feature extraction and ... Results indicate that signal processing methods may be very suitable for analyzing biological sequences. ...
... and a detailed research data report for RNA-Seq. The workflow can be executed on a standalone virtual machine or on a parallel ... MAP-RSeq: Mayo Analysis Pipeline for RNA Sequencing BMC Bioinformatics. 2014 Jun 27;15:224. doi: 10.1186/1471-2105-15-224. ... for a comprehensive analysis of RNA sequencing data. There is no one-stop shop for transcriptomic genomics. We have developed ... Several clinical and research projects at the Mayo Clinic have applied the MAP-RSeq workflow for RNA-Seq studies. The results ...
Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. Mei- ... Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing ... Thus, single-cell analyses reveal the dynamics of the stress response in terms of cell-specific RNA variants driving ... Data deposition: The sequencing short reads data have been deposited in the Sequence Read Archive at the National Center for ...
The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor. ... THE CRYSTAL STRUCTURE AND MUTATIONAL ANALYSIS OF A NOVEL RNA-BINDING DOMAIN FOUND IN THE HUMAN TAP NUCLEAR MRNA EXPORT FACTOR. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1KOH Legend Entity #1 , Chains: A,B,C,D TIP ASSOCIATING PROTEIN protein, ...
... expression profiling of samples from biobanks requires a method that can be used with intact as well as partially degraded RNA ... SureSelectXT RNA Direct: A Technique for Expression Analysis Through Sequencing of Target-Enriched FFPE Total RNA. ... "RNA Direct" that generates RNA-Seq data with minimal ribosomal contamination and good sequencing coverage. Using RNA isolated ... SureSelectXT RNA Direct for preparation of strand-specific sequencing libraries from high-quality or FFPE-derived RNA samples ...
RNA Sequencing Analysis Reveals Interactions between Breast Cancer or Melanoma Cells and the Tissue Microenvironment during ... Y. Zhang, K. Chen, S. A. Sloan et al., "An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular ... J. M. Saunus, M. C. J. Quinn, A.-M. Patch et al., "Integrated genomic and transcriptomic analysis of human brain metastases ... C. Trapnell, L. Pachter, and S. L. Salzberg, "TopHat: discovering splice junctions with RNA-Seq," Bioinformatics, vol. 25, no. ...
We describe a comparative sequence analysis algorithm for detecting novel structural RNA genes. The key idea is to test the ... Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes. A reliable general purpose ... A conserved coding region tends to show a pattern of synonymous substitutions, whereas a conserved structural RNA tends to show ... Noncoding RNA genes produce transcripts that exert their function without ever producing proteins. ...
We postulated that a combination of DECS analysis and next-generation sequencing (NGS) would improve detection efficiency and ... DECS (dsRNA isolation, exhaustive amplification, cloning, and sequencing) analysis has been shown to be capable of detecting ... indicating that the candidate sequence was that of BSSV itself. Our results suggest that a combination of DECS analysis and NGS ... and sequenced using NGS. A contig of 4,020 nucleotides (nt) that shared similarities with sequences from other Sobemovirus ...
Binding of IRE-BP to Its Cognate RNA Sequence: SFM Studies on a Universal RNA Backbone for the Analysis of RNA-Protein ... We have used an RNA consisting of the potato spindle tuber viroid (PSTVd) and 240 bp of doublestranded RNA derived from the GUS ... The in vitro transcribed RNA forms a rodlike structure of apparent 130 nm in length with a completely base paired central part ... The termini of the molecule consist of loops such that no blunt or staggered RNA ends are exposed. Suitable, asymmetrical ...
We have compared the nucleotide sequences of the small RNA segments of two attenuated, low-passage variants of the PIC virus ... f Sequence analysis of the small RNA segment of guinea pig-passaged Pichinde virus variants. * Authors: L Zhang, K Marriott, J ... We have compared the nucleotide sequences of the small RNA segments of two attenuated, low-passage variants of the PIC virus ...
Opportunity: Bioinformatician with focus on high throughput sequence data analysis (RNA-seq) & pathway analysis/modeling @ U. ... Bioinformatician with focus on high throughput sequence data analysis (RNA-seq) & pathway analysis/modeling @ U. of Bern, ... analysis and interpretation as well as pathway analysis and network modeling of the complex RNA-seq data generated within the ... Experience in pathway analyses or network modeling will be considered as an advantage. Furthermore, a strong background in at ...
We purified the epitope-tagged RNA-binding protein, Hfq, and its bound RNA by immunoprecipitation from the model pathogen, ... It will be valuable to scientists working on genetically tractable bacteria who are interested in the function of RNA-binding ... Author Summary The past decade has seen small regulatory RNA become an important new mediator of bacterial mRNA regulation. ... RNA sequencing Is the Subject Area "RNA sequencing" applicable to this article? Yes. No. ...
Abstract 4867: Comparative analysis of RNA sequencing methods for characterization of cancer transcriptomics. Ryan P. Abo, Ling ... Comparative analysis of RNA sequencing methods for characterization of cancer transcriptomics. [abstract]. In: Proceedings of ... Abstract 4867: Comparative analysis of RNA sequencing methods for characterization of cancer transcriptomics ... Abstract 4867: Comparative analysis of RNA sequencing methods for characterization of cancer transcriptomics ...
Comparative transcriptome analysis of A. carmichaelii with A. heterophyllum identified 20,232 orthogroups, representing 30,633 ... In order to understand the biosynthesis of secondary metabolites, Illumina-based deep transcriptome profiling and analysis was ... transcriptome analysis across multiple tissues is an attractive method to identify the molecular components involved for ... performed for four tissues (flower, bud, leaf, and root) of A. carmichaelii, resulting in 5.5 Gbps clean RNA-seq reads ...
RNA sequencing (RNA-seq) has revolutionized the study of gene expression in animals, plants and microorganisms. However, ... Gene Expression Analysis Using 3-RNA Sequencing. SPONSORED BY: Lexogen, Lexogen C.E. CREDITS: P.A.C.E. CE ... RNA sequencing (RNA-seq) has revolutionized the study of gene expression in animals, plants and microorganisms. However, ... RNA-seq and RNA-seq technologies, we used data from a subset of 20 samples that were previously used in a RNA-seq study of feed ...
Single cell RNA sequencing High-throughput Single cell data analysis CEL-Seq2 Next-generation sequencing ... Sagar, Herman J.S., Pospisilik J.A., Grün D. (2018) High-Throughput Single-Cell RNA Sequencing and Data Analysis. In: Vavouri T ... Here, we describe a customized high-throughput protocol for single-cell RNA-sequencing (scRNA-seq) combining flow cytometry and ... Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6(5): ...
PubMed journal article Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow ... Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer. Sci Rep. ... Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer.. Sci Rep ... Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer. Sci Rep. ...
Next Generation Sequencing: Transcriptome Analysis, and RNA-Seq. Upon completion of this module, you will be able to: describe ... Computer Lab: RNA-seq Data Analysis RNA-seq (English Subtitles). To view this video please enable JavaScript, and consider ... Computer Lab: RNA-seq Data Analysis RNA-seq (English Subtitles)22:02 ... This is the RNA-Seq analysis pipeline. We get the raw data, map reads, assemble transcripts, calculate transcript abundance, ...
RNA-sequencing technologies, which sequence the RNA molecules being transcribed in cells, allow us to explore the process of ... RNA-SEQUENCING ANALYSIS: READ ALIGNMENT AND DISCOVERY AND RECONSTRUCTION OF FUSION TRANSCRIPTS. ... One of the primary goals of RNA sequencing analysis is to reconstruct the full set of transcripts (isoforms) of genes that were ... In contrast to DNA sequence alignment, RNA-seq mapping algorithms have two additional challenges. First, any RNA-seq alignment ...
The top sequence is the reference (REF) sequence, whereas the remaining sequences are the cloned PB2 subgenomic RNAs of ... Sequence Analysis of In Vivo Defective Interfering-Like RNA of Influenza A H1N1 Pandemic Virus. Kazima Saira, Xudong Lin, Jay V ... Complete sequence analyses show that two defective interfering influenza viral RNAs contain a single internal deletion of a ... Sequencing and analysis.Viral RNA was extracted from nasopharyngeal specimens and amplified by multisegment reverse ...
... *Authors: * ... Shen, L., Liu, M., Liu, W., Cui, J., Li, C.Bioinformatics analysis of RNA sequencing data reveals multiple key genes in ... Shen, L., Liu, M., Liu, W., Cui, J., Li, C.Bioinformatics analysis of RNA sequencing data reveals multiple key genes in ... Shen, L., Liu, M., Liu, W., Cui, J., & Li, C. (2018). Bioinformatics analysis of RNA sequencing data reveals multiple key genes ...
The sRNA deep-sequencing approach used in this analysis provides an intuitive method to survey micropathogen prevalence in ... As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that ... As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that ... Illumina HiSeq2000 technology was utilized to perform deep sequencing of small RNAs (sRNAs) extracted from field-collected H. ...
Abstract 15820: Early and Pre-clinical Transcriptome Analysis by RNA Sequencing Identifies Mitochondrial Dysfunction and ... Abstract 15820: Early and Pre-clinical Transcriptome Analysis by RNA Sequencing Identifies Mitochondrial Dysfunction and ... Abstract 15820: Early and Pre-clinical Transcriptome Analysis by RNA Sequencing Identifies Mitochondrial Dysfunction and ... Abstract 15820: Early and Pre-clinical Transcriptome Analysis by RNA Sequencing Identifies Mitochondrial Dysfunction and ...
  • To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively spliced exons and isoforms and assesses confidence in these estimates. (nih.gov)
  • RNA sequencing (RNASeq) provides the ability to comprehensively assay the transcriptome in a high-throughput manner. (aacrjournals.org)
  • Here, we describe a customized high-throughput protocol for single-cell RNA-sequencing (scRNA-seq) combining flow cytometry and a nanoliter-scale robotic system. (springer.com)
  • RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. (biomedcentral.com)
  • This study seeks to validate and extend previous studies on the expression of TE exons by an integrative statistical analysis of high throughput RNA sequencing data. (biomedcentral.com)
  • Microarray was a high-throughput sequencing, but it was limited by countable numbers of lncRNAs, and all the probes were already known, which was the reason for refraining the technology from discovering novel lncRNAs. (jcancer.org)
  • Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. (biomedcentral.com)
  • Statistical analysis of high-throughput sequencing datasets composed of per feature counts showed that the ALDEx2 R package is a simple and robust tool, which can be applied to RNA-seq, 16S rRNA gene sequencing and differential growth datasets, and by extension to other techniques that use a similar approach. (biomedcentral.com)
  • The objective of many high-throughput sequencing studies is to identify those genes or features that make a significant difference between two or more conditions. (biomedcentral.com)
  • High-throughput RNA sequencing (RNA-seq) is a powerful and unbiased tool that allows detection of genome-wide transcriptional profiling. (aging-us.com)
  • Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencing technology. (rna-seqblog.com)
  • Dr. Batorsky works to enable researchers to answer biological questions with data-driven methods, such as analysis of high-throughput DNA and RNA sequencing data. (tuftsctsi.org)
  • Therefore, in recent years, high-throughput gene expression studies have changed from microarray technology to RNA-Seq technology. (studyres.com)
  • An important issue in high-throughput gene expression research is the clustering analysis of gene expression data. (studyres.com)
  • Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. (haldanessieve.org)
  • We applied a high throughput RNA sequencing (RNA-seq) strategy using Illumina GAIIx to characterize the entire retinal transcriptome from nondiabetic and from streptozotocin-treated mice 32 weeks after induction of diabetes. (molvis.org)
  • Small RNA-Seq can analyze thousands of small RNA molecules with a high throughput and specificity. (wikipedia.org)
  • Get more powerful data from single cells - detect more transcripts with the same sequencing depth, including both mRNA and lncRNA, providing deeper insights into the transcriptome and unveiling the expression of important regulatory RNAs. (qiagen.com)
  • In alternative expression analysis by sequencing (ALEXA-seq), we developed a method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. (nih.gov)
  • Incorporation of mRNA fragment length distribution in paired-end RNA-seq greatly improved estimation of alternative-splicing levels. (nih.gov)
  • Our results provide a probabilistic framework for RNA-seq analysis, give functional insights into pre-mRNA processing and yield guidelines for the optimal design of RNA-seq experiments for studies of gene and isoform expression. (nih.gov)
  • To examine a cost-effective alternative, we used a method, which confines sequencing to the 3'-end of mRNA and produces just one fragment per transcript, resulting in a dramatic decrease in sequencing cost. (labroots.com)
  • Messenger RNA (mRNA) has been the primary target of transcriptome studies. (biomedcentral.com)
  • now, RNA-seq is a way where we can actually assess the level of gene expression for any given organism, without a reference genome sequence, simply by extracting its RNA, its mRNA, sequencing it, And then, basically, looking for, matches to certain genes. (coursera.org)
  • Unsupervised clustering of samples by miRNA sequence families best reflected the clustering based on mRNA expression available for this sample set. (aacrjournals.org)
  • Here, we used RNA sequencing and proteomics to determine how alkaloids impact mRNA or protein abundance in the little devil frog ( Oophaga sylvatica ), and compared wild-caught chemically defended frogs with laboratory frogs raised on an alkaloid-free diet. (biologists.org)
  • It provides essential pipeline infrastructure for efficient and reproducible analysis of total RNA, poly(A)-derived RNA, small RNA, and integrated microRNA (miRNA) and mRNA data. (biomedcentral.com)
  • The course covers methods to process raw data from genome-wide mRNA expression studies (microarrays and RNA-seq) including data normalization, differential expression, clustering, enrichment analysis and network construction. (coursera.org)
  • Our results indicate that, while the current long-read protocol is considerably more expensive than short-read sequencing, there are important benefits that can only be achieved with longer read length, including lower mapping bias and reduced ambiguity in assigning reads to genomic elements, such as mRNA transcript. (haldanessieve.org)
  • The item "small RNA" is a rather arbitrary term, which is vaguely defined based on its length comparing with regular RNA such as messenger RNA (mRNA). (wikipedia.org)
  • We further demonstrate that drug-tolerant cells contain specific RNA variants residing in genes involved in microtubule organization and stabilization, as well as cell adhesion and cell surface signaling. (pnas.org)
  • Noncoding RNA genes produce transcripts that exert their function without ever producing proteins. (biomedcentral.com)
  • Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes. (biomedcentral.com)
  • A reliable general purpose computational genefinder for noncoding RNA genes has been elusive. (biomedcentral.com)
  • We describe a comparative sequence analysis algorithm for detecting novel structural RNA genes. (biomedcentral.com)
  • Tests suggest that this approach detects noncoding RNA genes with a fair degree of reliability. (biomedcentral.com)
  • The number and diversity of ncRNA genes remains poorly understood, despite the availability of many complete genome sequences. (biomedcentral.com)
  • New noncoding RNA genes continue to be discovered by less systematic means, which makes it seem likely that a systematic RNA genefinding algorithm would be of use. (biomedcentral.com)
  • Nonetheless, conserved RNA secondary structure remained our best hope for an exploitable statistical signal in ncRNA genes. (biomedcentral.com)
  • One of the primary goals of RNA sequencing analysis is to reconstruct the full set of transcripts (isoforms) of genes that were present in the original cells. (umd.edu)
  • In the present study, the RNA sequencing (RNA‑seq) data of uterine corpus endometrial carcinoma (UCEC) samples were collected and analyzed using bioinformatics tools to identify potential genes associated with the development of UCEC. (spandidos-publications.com)
  • Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was also performed on the DEGs using KOBAS 2.0 software. (spandidos-publications.com)
  • In accord with the RNA-Seq data, mitochondrial electron transport chain activity of complex I was significantly reduced, as were the transcripts levels of the nuclear genes encoding complex I proteins. (ahajournals.org)
  • Targeted sequencing is a technique in which a subgroup of genes or regions of the genome are isolated and sequenced. (express-press-release.net)
  • Next-generation sequencing (NGS) is a technique that plays important role in targeted sequencing and offers the resolution, scalability, and speed to assess targeted genes of interest. (express-press-release.net)
  • DAVID analyses showed that genes upregulated in an IA size-associated module were enriched with genes involved in cellular respiration and translation, while genes involved in transcription were down-regulated in a module associated with ruptured IAs. (ahajournals.org)
  • Recent developments in DNA and RNA sequencing technologies have allowed for the detection of genes and mutations involved in mitochondrial function and also for the analysis of how mitochondrial genome processing varies across human individuals and populations. (findaphd.com)
  • Here, we use single molecule RNA FISH measurements of 26 genes in thousands of melanoma cells to provide an independent reference dataset to assess the performance of the DropSeq and Fluidigm single cell RNA sequencing platforms. (fluidigm.com)
  • We quantified the Gini coefficient, a measure of rare-cell expression variability, and find that the correspondence between RNA FISH and single cell RNA sequencing for Gini, unlike for mean, increases markedly with per-cell library complexity up to a threshold of ~2000 genes detected. (fluidigm.com)
  • RNA-sequencing (RNA-seq) data from eight equine tissue samples (34-day whole embryo, full term placental villous, adult testes, adult cerebellum, adult articular cartilage, adult LPS-stimulated articular cartilage, adult synovial membrane, and adult LPS-stimulated synovial membrane) were used to refine the structural annotation of protein-coding genes in the horse and for a preliminary assessment of tissue-specific expression patterns. (biomedcentral.com)
  • A consensus set of equine protein-coding gene structures was defined by consolidation of gene sets predicted by Ensembl and NCBI (containing 20,322 and 17,610 genes respectively) and structural annotation derived from the RNA-seq experiments. (biomedcentral.com)
  • Using RNA interference (RNAi), prior work found that knockdown of Osiris family genes Osiris 6 ( Osi6 ), Osi7 , and Osi8 led to increased susceptibility to OA in adult D. melanogaster flies, likely representing genes underlying a Quantitative Trait Locus (QTL) for OA resistance in D. sechellia . (g3journal.org)
  • Here, we identify new candidate OA resistance genes by performing differential gene expression analysis using RNA-sequencing (RNA-seq) on control and OA-exposed D. sechellia flies. (g3journal.org)
  • We found 104 significantly differentially expressed genes with annotated orthologs in D. melanogaster , including six Osiris gene family members, consistent with previous functional studies and gene expression analyses. (g3journal.org)
  • The information contained in the genome of an organism, its DNA, is expressed through transcription of its genes to RNA, in quantities determined by many internal and external factors. (helsinki.fi)
  • Bioinformatic analyses revealed significantly upregulated expression of genes encoding plasma membrane solute carrier proteins in FRDA fibroblasts. (curefa.org)
  • More than a quarter of all sequence reads mapping outside of ribosomal RNA genes represent non-coding RNA, and the density of reads mapping to intergenic regions was more than two-fold higher than that mapping to annotated coding sequences. (ucl.ac.uk)
  • The ALDEx2 approach is shown to be suitable for all three types of data: it correctly identifies both the direction and differential abundance of features in the differential growth experiment, it identifies a substantially similar set of differentially expressed genes in the RNA-seq dataset as the leading tools and it identifies as differential the taxa that distinguish the tongue dorsum and buccal mucosa in the Human Microbiome Project dataset. (biomedcentral.com)
  • The entities can be genes, other expressed or non-expressed genomic features (RNA-seq and metagenomics), operational taxonomic units (OTUs) (16S rRNA gene sequencing) or genomic segments (ChIP-seq). (biomedcentral.com)
  • We present evidence that miRNA precursors are present in the single-celled green alga Chlamydomonas reinhardtii and that they give rise to mature miRNAs that regulate target genes by post-transcriptional RNA cleavage. (technologynetworks.com)
  • However, RNA sequencing technology has revealed that the human genome is pervasively transcribed, resulting in thousands of novel non-coding RNA genes. (biomedcentral.com)
  • The majority of the methods suggest removal of low expressed genes before the start of data analysis, but this procedure essentially blocks researchers from studying lncRNAs. (biomedcentral.com)
  • RNA sequence analysis further revealed that SNAI1 knockdown decreased the expression of genes related to cytoskeleton rearrangement and ECM remodeling. (springer.com)
  • We first estimated cell-type proportions among AD, MCI, and CN samples from the bulk RNA-seq data using CIBERSORT and then examined the differentially expressed genes (DEGs) between AD and CN samples. (biomedcentral.com)
  • In addition, GSEA and network-based meta-analysis based on DEGs between AD and CN samples revealed functional modules and important hub genes associated with the pathogenesis of AD. (biomedcentral.com)
  • In the present study, for the first time, researchers at the State Forestry Administration , China performed de novo transcriptome sequencing and mapped to the moso bamboo genomic resources (reference genome and genes) to produce a comprehensive dataset for the fast growing shoots of moso bamboo. (rna-seqblog.com)
  • Using next-generation RNA-sequencing, we characterized the transcriptomes of these phenotypically similar, but biologically distinct, leukemias, identifying hundreds of differentially expressed genes and a large number of structural differences (eg, alternative splicing and promoter usage). (bloodjournal.org)
  • It is even more amazing to consider that this machine, in addition to containing the genes for it's own construction (basically that the genome IS the entity that replicates), also contain the genetic sequences that encodes the tRNA molecules. (theleagueofreason.co.uk)
  • We suggest that the ribosome may represent one important missing link between compositional (or metabolism-first), RNA-world (or genes-first) and cellular (last universal common ancestor) approaches to the evolution of cells. (theleagueofreason.co.uk)
  • Gene ontology (GO) and KEGG pathway enrichment analyses were applied, and protein-protein interaction (PPI) networks and Cytoscape software were utilized to identify key genes. (current-gene-therapy.com)
  • Gene Expression Data The purpose of clustering analysis is to cluster together genes with the same or similar functions. (studyres.com)
  • CAS genes also shared a promoter structure comprising modules proximal and distal to the coding sequence. (plantphysiol.org)
  • Although the costs of next generation sequencing technology have decreased over the past years, there is still a lack of simple-to-use applications, for a comprehensive analysis of RNA sequencing data. (nih.gov)
  • We postulated that a combination of DECS analysis and next-generation sequencing (NGS) would improve detection efficiency and usability of the technique. (mdpi.com)
  • Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. (jove.com)
  • However, in a little over a decade since its inception, Next-Generation Sequencing (NGS) technology has made it possible to sequence the entire human genome within two weeks and for US $1,000. (jove.com)
  • Clearly, RNA-Seq analysis is vulnerable to the general biases and errors inherent in the next-generation sequencing (NGS) technology upon which it is based. (biomedcentral.com)
  • Next-generation sequencing was applied in 7 cases of NPC tissues and 7 cases of normal tissues in nasopharynx. (jcancer.org)
  • So today we are doing a bit of meta genomics, which has really taken off in the past five years due to the awesome power of next generation sequencing and the awesome cheapness of next generation sequencing. (coursera.org)
  • Another thing that we'll be looking at with, next generation sequencing, is some RNA-seq data. (coursera.org)
  • His research work focuses on providing current research technology to basic research community within and outside of the University, including next generation sequencing (NGS), high throughout screen (HTS), high content screen (HGS), robotics automation and flow cytometry. (tuftsctsi.org)
  • With a dynamic range to detect subtle changes in expression level in a hypothesis neutral environment, next generation sequencing enables the understanding of biological response to stimuli or environmental changes. (thermofisher.com)
  • Recommended RNA purification kit for next generation sequencing applications. (thermofisher.com)
  • RNA-Seq is a sequencing technique applied to transcript analysis by next-generation sequencing technology, and can be applied to the study of gene expression. (studyres.com)
  • Since the development of next-generation sequencing technology, RNA-Seq data are generally considered to have advantages over conventional microarray (microarray) gene expression data, including the large dynamic range of gene expression values and the low Of the background noise and other characteristics. (studyres.com)
  • To define gene expression changes associated with diabetic retinopathy in a mouse model using next generation sequencing, and to utilize transcriptome signatures to assess molecular pathways by which pharmacological agents inhibit diabetic retinopathy. (molvis.org)
  • Next generation sequencing-based RNA-seq profiles provided comprehensive signatures of transcripts that are altered in early stages of diabetic retinopathy. (molvis.org)
  • The ideal candidate has a PhD in bioinformatics, biology, computer science, or a related field with proven expertise in the management and analysis of large-scale datasets. (bioinformatics.org)
  • However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. (jove.com)
  • The studentship is centered on the computational analysis of large multi-omic datasets, with the aim of unravelling variation and key processes influencing mitochondrial function. (findaphd.com)
  • Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. (biomedcentral.com)
  • These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. (biomedcentral.com)
  • We collected 26 RNA-seq datasets spanning multiple tissues and cancer types. (biomedcentral.com)
  • Fifteen performance metrics are used to evaluate DE tools and normalization methods using simulations and analyses of six diverse RNA-seq datasets. (biomedcentral.com)
  • All the pipelines exhibit inferior performance for lncRNAs compared to mRNAs across all simulated scenarios and benchmark RNA-seq datasets. (biomedcentral.com)
  • Furthermore, the accuracy of existing tools often varies across datasets and data types, making a consensus on best practices for processing and analysing sequenced data challenging to reach. (biomedcentral.com)
  • In this study, we generated two paired-end RNA-seq datasets of differing read lengths (2×75 bp and 2×262 bp) for lymphoblastoid cell line GM12878 and compared the effect of read length on transcriptome analyses, including read-mapping performance, gene and transcript quantification, and detection of allele-specific expression (ASE) and allele-specific alternative splicing (ASAS) patterns. (haldanessieve.org)
  • We have developed MAP-RSeq, a comprehensive computational workflow that can be used for obtaining genomic features from transcriptomic sequencing data, for any genome. (nih.gov)
  • Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance," Journal of Pathology , vol. 237, no. 3, pp. 363-378, 2015. (hindawi.com)
  • Badger & Olsen use the BLASTN program [ 17 ] to locate genomic regions with significant sequence similarity between two related bacterial species. (biomedcentral.com)
  • The presence of high molecular weight double-stranded RNA (dsRNA) within plant cells is an indicator of infection with RNA viruses as these possess genomic or replicative dsRNA. (mdpi.com)
  • A contig of 4,020 nucleotides (nt) that shared similarities with sequences from other Sobemovirus species was obtained as a candidate of the BSSV genomic sequence. (mdpi.com)
  • Even though several technical challenges remain to be addressed to exploit the potential of the nanopore technology fully, our work illustrates that DRS may significantly advance genomic studies of complex virus populations, including predictions on long-range interactions in individual full-length viral RNA haplotypes. (nanoporetech.com)
  • Heterogeneity was found at both the genomic and RNA level at position 1352. (microbiologyresearch.org)
  • miRNAs were organized in genomic clusters representing promoter-controlled miRNA expression and sequence families representing seed sequence-dependent miRNA target regulation. (aacrjournals.org)
  • Many of the NGS sequencing protocols rely on the production of a genomic library that contains thousands of fragments of the target nucleic acids that will then be sequenced by proper technologies. (wikipedia.org)
  • Using SureSelect XT RNA Direct protocol (RNA Direct) workflow, we found transcripts to be upregulated or downregulated to similar degrees with similar confidence levels in both the FF and FFPE samples, demonstrating the utility for meaningful gene expression studies with biobank samples of variable quality. (springer.com)
  • Halvardson J, Zaghlool A, Feuk L (2013) Exome RNA sequencing reveals rare and novel alternative transcripts. (springer.com)
  • We have inserted the IRE (iron responsive element) sequence into the construct and have used in vitro transcripts to study binding of IREBP. (degruyter.com)
  • While the data indicated that capture-based protocols provided efficient methods for sampling transcripts as compared to whole-transcriptome RNA-seq, there are considerations in its use, particularly for duplicate reads and uncaptured transcripts. (aacrjournals.org)
  • RNA-based Targeted Sequencing is a technique for sequencing and selecting specific pathways or transcripts of interest of gene expression microarray. (express-press-release.net)
  • RNA-seq, on the other hand, can be used to detect both known and unknown transcripts while producing low background noise due to its unambiguous DNA mapping nature. (jove.com)
  • Long non-coding RNAs(lncRNAs) previously were considered as "transcriptional noise", which accounted for at least 75% of DNA transcripts[ 4 ]. (jcancer.org)
  • RNA sequencing provides a new perspective on the genome of Mycobacterium tuberculosis by revealing an extensive presence of non-coding RNA, including long 5' and 3' untranslated regions, antisense transcripts, and intergenic small RNA (sRNA) molecules. (ucl.ac.uk)
  • Conversely, the nuclear fraction shows an enrichment of unprocessed RNA compared with total RNA-seq, making it suitable for analysis of nascent transcripts and RNA processing dynamics. (biomedcentral.com)
  • Recently, two technologies, the genome-wide nuclear run-on sequencing (GRO-seq) and native elongating transcript sequencing (NET-seq), have been described to study nascent transcripts. (biomedcentral.com)
  • The comparison of RNA-seq with microarray in quantifying gene expression level has been carried out in schistosoma-induced pulmonary hypertension, which showed that the correlation between microarray and RNA-seq was lower, especially for low copy transcripts where RNA-seq had a wider dynamic range than microarray [ 6 ]. (aging-us.com)
  • With the PrimeFlow assay, researchers can now incorporate the simultaneous analysis of RNA transcripts and proteins to elevate their understanding of single-cell dynamics, the company said. (genomeweb.com)
  • With nanopore sequencing, read length is equal to fragment length, enabling routine analysis of long, full-length transcripts. (londoncallingconf.co.uk)
  • This minimises the impact of multimapping - where short sequencing reads align to multiple locations - and allows complete characterisation of transcript isoforms and chimeric transcripts. (londoncallingconf.co.uk)
  • The facility to sequence full-length transcripts enables modifications to be unambiguously assigned to specific isoforms. (londoncallingconf.co.uk)
  • Our studies clearly demonstrate RNA-seq as a comprehensive strategy for identifying disease-specific transcripts, and for determining comparative profiles of molecular changes mediated by candidate drugs. (molvis.org)
  • MIRA is available at https://github.com/comprna/mira Implications: The study of recurrent cancer mutations on potential RBP binding sites reveals new alterations in introns, untranslated regions, and long non-coding RNAs, that impact RNA processing and provide a new layer of insight that can aid in the interpretation of non-coding variants in cancer genomes. (aacrjournals.org)
  • Xiao G , Wang T , Zhuang W , Ye C , Luo L , Wang H , Lian G , Xie L , . RNA sequencing analysis of monocrotaline-induced PAH reveals dysregulated chemokine and neuroactive ligand receptor pathways. (aging-us.com)
  • Comparative transcriptome analysis of A. carmichaelii with A. heterophyllum identified 20,232 orthogroups, representing 30,633 unigenes of A. carmichaelii , gene ontology enrichment analysis of which revealed essential biological process together with a secondary metabolic process to be highly enriched. (mdpi.com)
  • Amplicon generation and target enrichment are the two important methods used for Targeted DNA/RNA Sequencing that could be explored in forecast period. (express-press-release.net)
  • This protocol provides stepwise instructions for using the various Galaxy modules for accessing raw NGS data, quality-control checks, alignment, and differential gene expression analysis, guiding the user with parameters at every step to generate a gene list that can be screened for enrichment of gene classes or biological processes using DAVID. (jove.com)
  • Our results show that cellular fractionation is a more rapid and cost effective approach than conventional polyA+ enrichment when studying mature RNAs. (biomedcentral.com)
  • Functional enrichment analysis of DEGs showed inflammatory/immune response occurred in the early stage of PAH development. (aging-us.com)
  • KEGG pathway enrichment analysis of DEGs showed that cytokine-cytokine receptor interaction and neuroactive ligand-receptor interaction were in the initiation and progression of PAH. (aging-us.com)
  • To gain further insight into the biological functions of the DEGs, we performed gene set enrichment analysis (GSEA) and network-based meta-analysis. (biomedcentral.com)
  • Enrichment analyses identified elevations in glutathione regulation, insulin signaling, and mitochondrial metabolism in nonresponders pretraining, which was reflected in vivo by higher pretraining PCr recovery rate and insulin sensitivity in these same individuals. (diabetesjournals.org)
  • Enrichment of the true whole transcriptome through selective depletion of 99.9% of ribosomal RNA. (thermofisher.com)
  • Although the applicability of small subunit ribosomal RNA (16S rRNA) sequences for bacterial classification is now well accepted, the general use of these molecules has been hindered by the technical difficulty of obtaining their sequences. (pnas.org)
  • RNA-sequencing technologies, which sequence the RNA molecules being transcribed in cells, allow us to explore the process of transcription in exquisite detail. (umd.edu)
  • These lncRNAs form a large and diverse class of transcribed RNA molecules, constituting up to 70% of the transcriptome with a defined length of 200 nucleotides. (biomedcentral.com)
  • Both forms of RNA represent heterogeneous pools of RNA molecules at different levels of maturation and processing. (biomedcentral.com)
  • At any given time, a wide range of different RNA molecules are present at different levels of maturation and processing. (biomedcentral.com)
  • It turns out the ribosome contains nucleotide sequences of all 20 tRNA molecules, several ribosomal proteins, RNA polymerases and a host of other entities. (theleagueofreason.co.uk)
  • That the ribosome itself contain the sequences for tRNA molecules carrying all 20 amino acids? (theleagueofreason.co.uk)
  • Base modifications such as m6A can modulate the activity and stability of RNA molecules, and have been linked to multiple human diseases and antimicrobial resistance. (londoncallingconf.co.uk)
  • Unlike traditional technologies, nanopore technology can sequence native RNA molecules. (londoncallingconf.co.uk)
  • Small RNA sequencing (Small RNA-Seq) is a type of RNA sequencing based on the use of NGS technologies that allows to isolate and get information about noncoding RNA molecules in order to evaluate and discover new forms of small RNA and to predict their possible functions. (wikipedia.org)
  • Small RNAs are noncoding RNA molecules between 20 and 200 nucleotide in length. (wikipedia.org)
  • After this step an aliquot of chloroform is added in order to separate the aqueous phase (containing the RNA molecules) from the organic phase (cellular debris and other contaminants). (wikipedia.org)
  • spin column chromatography: universally used method to purify nucleic acids that exploits a spin column containing a special resin that, after a first step of cell lysis, allows the binding of the RNA molecules, eluting unbound particles (several proteins and rRNA). (wikipedia.org)
  • This method can separate small RNA molecules without the need of adding phenol. (wikipedia.org)
  • After the adapters are ligated to both ends of the small RNAs, retrotranscription occurs producing complementary DNA molecules (cDNAs) which will be, eventually, amplified by different amplification techniques depending on the sequencing protocol that is being followed (Ion Torrent exploits the emulsion PCR, while Illumina requires a bridge PCR) in order to obtain up to billions of amplicons to be sequenced. (wikipedia.org)
  • This report investigates the possibility of using signal processing techniques in the analysis of biological sequences: DNA, RNA and proteins. (psu.edu)
  • We have used an RNA consisting of the potato spindle tuber viroid (PSTVd) and 240 bp of doublestranded RNA derived from the GUS gene as a backbone for scanning force microscope (SFM) studies on RNA binding proteins. (degruyter.com)
  • It thus provides a versatile tool to study specific as well as preferential interaction of other proteins with sequences or structures inserted into a different part of the molecule. (degruyter.com)
  • Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. (jalview.org)
  • Therefore, we developed a new method, MIRA (Mutation Identification for RNA Alterations), to perform an unbiased and comprehensive study of significantly mutated regions (SMRs) affecting binding sites for RNA-binding proteins (RBPs) in cancer. (aacrjournals.org)
  • EDEN-BP contains three RNA recognition motifs (RRMs) and is related to the elav family of RNA-binding proteins. (semanticscholar.org)
  • A non-redundant, curated database of human RNA binding proteins (RBPs). (omictools.com)
  • Provides access to information on all RNA-binding proteins (RBPs) from the model organism E. coli. (omictools.com)
  • Provides access to known human RNA-binding proteins (RBPs). (omictools.com)
  • eBioscience, an Affymetrix business, announced the availability of the PrimeFlow RNA Assay, a flow cytometry assay capable of simultaneously detecting RNA and proteins within millions of cells at single-cell resolution. (genomeweb.com)
  • Even more amazingly, some of the proteins that coat the ribosome and aid it in it's translation of messenger-RNA, are themselves encoded in RNA nucleotide sequence, in the ribosomal RNA. (theleagueofreason.co.uk)
  • Although the small sample size prevents us from drawing definite conclusions, we observed promising novel co-expression networks for IAs: WCGNA analysis showed down-regulation of two transcript modules associated with ruptured IA status (r=-0.78, p=0.008 and r=-0.77, p=0.009), and up-regulation of two modules associated with aneurysm size (r=0.86, p=0.002 and r=0.9, p=4e-04), respectively. (ahajournals.org)
  • Although scRNA-seq protocols share common principles of single-cell isolation, cell lysis, transcript capture, complementary DNA (cDNA) conversion and amplification, library preparation, and sequencing, the methodologies differ. (biomedcentral.com)
  • A common analysis workflow of RNA-sequencing (RNA-seq) data consists of mapping the sequencing reads to a reference genome, followed by the transcript assembly and quantification based on these alignments. (helsinki.fi)
  • Arguably, the most popular use of RNA-Seq is profiling of gene expression or transcript abundance between samples or differential expression (DE). (biomedcentral.com)
  • The high yields of long, full-length reads delivered by nanopore sequencing allow unambiguous characterisation and quantification of transcript isoforms - providing a true reflection of gene expression. (londoncallingconf.co.uk)
  • A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16S rRNA or cloning of its gene. (pnas.org)
  • and data analysis, storage, and management. (openpr.com)
  • However, dearth of skilled professionals and problems associated with storage of sequencing data restrain the market growth. (openpr.com)
  • Protocol modifications to the Agilent Strand-Specific RNA Library Prep kit resulted in a new workflow called "RNA Direct" that generates RNA-Seq data with minimal ribosomal contamination and good sequencing coverage. (springer.com)
  • Using RNA isolated from a set of matched samples including fresh frozen (FF) or formalin-fixed, paraffin-embedded (FFPE) from tumor/normal tissues we generated high-quality data using a protocol that does not require upfront ribosomal depletion or poly(A) selection. (springer.com)
  • The main responsibility of the jobholder will be the design, analysis and interpretation as well as pathway analysis and network modeling of the complex RNA-seq data generated within the project. (bioinformatics.org)
  • In particular, experience with sequencing data (e.g. (bioinformatics.org)
  • The analysis pipeline consists of a sequence of functions and tools to process and clean the raw data, generate quality control and summary metrics, and perform secondary analyses that include expression quantification, fusion detection and somatic mutation calling. (aacrjournals.org)
  • To compare gene expression measures between 3'-RNA-seq and RNA-seq technologies, we used data from a subset of 20 samples that were previously used in a RNA-seq study of feed efficiency. (labroots.com)
  • Since scRNA-seq requires amplification of a low amount of endogenous cellular RNA, leading to substantial technical noise in the dataset, downstream data filtering and analysis require special care. (springer.com)
  • Therefore, we also briefly describe in-house state-of-the-art data analysis algorithms developed to identify cellular subpopulations including rare cell types as well as to derive lineage trees by ordering the identified subpopulations of cells along the inferred differentiation trajectories. (springer.com)
  • Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. (unboundmedicine.com)
  • explore how the RNA-seq data were analyzed. (coursera.org)
  • This is the RNA-Seq data for Drosophila melanogaster.We have downloaded its genome in advance, which is this file.Let's take a look. (coursera.org)
  • UCEC RNA‑seq data were downloaded from The Cancer Genome Atlas database. (spandidos-publications.com)
  • The resultant sRNA library data revealed that the surveyed tick populations produced reads that were homologous to St. Croix River Virus (SCRV) sequences. (frontiersin.org)
  • The technique enables researchers to analyze data, focus time, and expenses on target areas of interest and allows sequencing at advanced exposure levels. (express-press-release.net)
  • Moreover, targeted gene sequencing makes the study easier and produces smaller and manageable data set. (express-press-release.net)
  • Galaxy and DAVID have emerged as popular tools that allow investigators without bioinformatics training to analyze and interpret RNA-Seq data. (jove.com)
  • This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets. (jove.com)
  • We describe a straightforward workflow that will help C. elegans researchers to isolate worm RNA, conduct an RNA-Seq experiment and analyze the data using Galaxy and DAVID platforms. (jove.com)
  • New NGS instruments that allow ever-increasing speeds of sequencing-data collection with incredible efficiency, along with sharp reductions in cost, are revolutionizing modern biology in unimaginable ways as genome sequencing projects are rapidly becoming commonplace. (jove.com)
  • However, significant challenges remain that make NGS inaccessible to the wider scientific community, including limitations of storage, processing, and most of all, meaningful bioinformatics analysis of large volumes of sequencing data. (jove.com)
  • The rapid advances in sequencing technologies and exponential data accumulation have created a great need for computational platforms that will allow researchers to access, analyze and understand this information. (jove.com)
  • Early systems were heavily dependent upon computer programming knowledge, whereas, genome browsers such as NCBI that allowed non-programmers to access and visualize data did not permit sophisticated analyses. (jove.com)
  • Initially the project will focus on combining large amounts of RNA sequencing data to determine the genetic drivers of post-transcriptional processes in human mitochondria via genome-wide association studies. (findaphd.com)
  • In the opposite situation, RNA-seq data identified 215 transcriptional units with strong homology to known mammalian gene sequences, but not included in the in silico equine gene sets. (biomedcentral.com)
  • In this study, we first conducted a comprehensive analysis of the modeling UMI counts and read counts in scRNA-seq data. (biomedcentral.com)
  • The first part of this thesis focuses on the analysis of short-read RNA-seq data. (helsinki.fi)
  • The second part, where the main contributions of this thesis lie, focuses on the analysis of long-read RNA-seq data. (helsinki.fi)
  • Extracting signals related to RNA-related selection processes and using RNA sequencing (RNA-seq) data from the same specimens, we identified alterations in RNA expression and splicing linked to mutations on RBP binding sites. (aacrjournals.org)
  • Existing knowledge of the retention patterns of TE exons in mRNAs were mainly established by the analysis of Expressed Sequence Tag (EST) data and microarray data. (biomedcentral.com)
  • The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (ucl.ac.uk)
  • In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. (biomedcentral.com)
  • Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. (biomedcentral.com)
  • Compositional data analysis methods transform the data to relative abundances with the result that the analyses are more robust and reproducible. (biomedcentral.com)
  • Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a compositional data analysis tool that uses Bayesian methods to infer technical and statistical error. (biomedcentral.com)
  • In this study, the performance of 25 pipelines for testing DE in RNA-seq data is comprehensively evaluated, with a particular focus on lncRNAs and low-abundance mRNAs. (biomedcentral.com)
  • Furthermore, several studies [ 7 - 9 ] demonstrated that lncRNA expression levels are very noisy, which is a characteristic shared with low count data from massively parallel RNA sequencing. (biomedcentral.com)
  • To our knowledge, no statistical method has been specifically developed for the analysis of lncRNA-seq data and therefore transcriptome studies make use of statistical methods that assume sufficient expression levels. (biomedcentral.com)
  • In this paper, we evaluated and compared the performance of many popular statistical methods (Table 1 ) developed for testing DGE of RNA-seq data (hereafter referred to as "DE tools"), with special emphasis on lncRNAs and low-abundance mRNAs. (biomedcentral.com)
  • Such heterogeneity, in addition to the biases associated with polyA+ purification steps, may influence the analysis, sensitivity and the interpretation of RNA-seq data. (biomedcentral.com)
  • In comparison with conventional polyA+ RNA, the cytoplasmic RNA contains a significantly higher fraction of exonic sequence, providing increased sensitivity in expression analysis and splice junction detection, and in improved de novo assembly of RNA-seq data. (biomedcentral.com)
  • The data can be used to select target gene products for detailed characterization and to serve as starting points for identifying sequence homologues in other microbial proteomes. (omictools.com)
  • How to Analyze RNA-Seq Data? (rna-seqblog.com)
  • In recent years, various tools for analyzing single-cell RNA-sequencing data have been proposed, many of them with the purpose of performing differentially expression analysis. (rna-seqblog.com)
  • In this work, we compare four different tools for single-cell RNA-sequencing differential expression, together with two popular methods originally developed for the analysis of bulk RNA-sequencing data, but largely applied to single-cell data. (rna-seqblog.com)
  • Globally, the results obtained in our study suggest that is difficult to identify a best performing tool and that efforts are needed to improve the methodologies for single-cell RNA-sequencing data analysis and gain better accuracy of results. (rna-seqblog.com)
  • Which method should you use for normalization of RNA-Seq data? (rna-seqblog.com)
  • Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. (coursera.org)
  • Topics covered include multiple sequence alignments, phylogenetics, gene expression data analysis, and protein interaction networks, in two separate parts. (coursera.org)
  • In this module we'll explore some of the data that have been generated as a result of the rapid decrease in the cost of sequencing DNA. (coursera.org)
  • We'll be exploring a couple of RNA-Seq data sets that can tell us where any given gene is expressed, and also how that gene might be alternatively spliced. (coursera.org)
  • In this study, we compare, for the first time, existing TC RNA-seq tools on an extensive simulation data set and validated the best performing tools on published data. (ethz.ch)
  • In addition, it has several facilities to visualize and compare data that are derived from multiple solutions for one sequence or multiple solutions from several sequences. (biomedcentral.com)
  • This session will introduce methods for analyzing and visualizing RNA-seq data: quality control, alignment-based quantification, transcriptome assembly and differential expression analysis. (tuftsctsi.org)
  • We used RNA sequencing data analysis of cultured adipocytes to screen factors secreted in response to recombinant IL-13. (diabetesjournals.org)
  • 2005), the past major research is the microarray gene expression data cluster analysis. (studyres.com)
  • This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. (biomedcentral.com)
  • Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. (biomedcentral.com)
  • It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. (biomedcentral.com)
  • SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. (biomedcentral.com)
  • Massively parallel cDNA sequencing technology (RNA-seq) generates vast amounts of biological data and has become a primary means of transcriptome analysis. (biomedcentral.com)
  • A number of RNA-seq protocols exist to produce total RNA, poly(A)-derived RNA and small RNA data. (biomedcentral.com)
  • These tools represent commonly known and established methods developed for sequencing data. (biomedcentral.com)
  • The course presents software tools developed by the Ma'ayan Laboratory (http://labs.icahn.mssm.edu/maayanlab/) from the Icahn School of Medicine at Mount Sinai, but also other freely available data analysis and visualization tools. (coursera.org)
  • A set of lectures in the 'Deep Sequencing Data Processing and Analysis' module will cover the basic steps and popular pipelines to analyze RNA-seq and ChIP-seq data going from the raw data to gene lists to figures. (coursera.org)
  • We analyzed human whole blood transcriptomes by performing paired-end, 100 bp RNA-sequencing (RNAseq) using the Illumina platform. (ahajournals.org)
  • NGS-based RNA-Seq in particular has made it possible to identify and map transcriptomes comprehensively with accuracy and sensitivity, and has replaced microarray technology as the method of choice for expression profiling. (jove.com)
  • Herein, we conducted unbiased RNA sequencing to profile the transcriptomes of fibroblast cell lines derived from 18 FRDA patients and 17 unaffected control individuals. (curefa.org)
  • Thus, RNA-seq of separated cytosolic and nuclear RNA can significantly improve the analysis of complex transcriptomes from mammalian tissues. (biomedcentral.com)
  • The sequencing of the transcriptomes of single-cells, or single-cell RNA-sequencing, has now become the dominant technology for the identification of novel cell types and for the study of stochastic gene expression. (rna-seqblog.com)
  • RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. (haldanessieve.org)
  • We have developed an in situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved cells and tissue. (nih.gov)
  • In RNA-Seq, mRNAs are split into small fragments, filtered by length, and sequenced. (coursera.org)
  • This procedure provides a gel electrophoresis "ladder" of hydrolyzed RNA fragments. (thermofisher.com)
  • All of these study designs share common aspects whereby DNA fragments are incorporated into a library, a small proportion of that library is sequenced on an instrument and the reads from the sequencing run are binned into features that represent an underlying biological entity. (biomedcentral.com)
  • long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. (rna-seqblog.com)
  • The greatest advantage of using RNA-seq is represented by the possibility of generating libraries of RNA fragments starting from the whole RNA content of a cell. (wikipedia.org)
  • This step is very critical and important for any molecular-based technique since it ensures that the small RNA fragments found in the samples to be analyzed are characterized by a good level of purity and quality. (wikipedia.org)
  • Jones J.C., Siebold A.P., Livi C.B., Lucas A.B. (2018) SureSelect XT RNA Direct: A Technique for Expression Analysis Through Sequencing of Target-Enriched FFPE Total RNA. (springer.com)
  • Total RNA isolated from chicken adipose tissue samples was used for cDNA library preparation using QuantSeq 3'mRNA-seq library Prep Kit. (labroots.com)
  • Total RNA was extracted, cDNA library was constructed, and cDNAs were amplified and sequenced. (springermedizin.de)
  • The starting material for RNA sequencing (RNA-seq) studies is usually total RNA or polyA+ RNA. (biomedcentral.com)
  • Although total RNA-seq has been shown to provide insight into ongoing transcription and co-transcriptional splicing in the nucleus [ 14 , 20 ], the simultaneous presence of mature RNAs from the cytoplasm confounds the analysis of nuclear RNA maturation steps. (biomedcentral.com)
  • Here, we describe the cloning and isolation of HCV replicon-bearing cells, the extraction of total RNA, the generation of cDNA, and the amplification of specific HCV replicon sequences for sequence analysis. (scripps.edu)
  • The Ion Total RNA-Seq Kit v2 provides a fast, simple workflow with as little as 100 ng of total RNA input, while maintaining strand orientation and minimizing bias and error. (thermofisher.com)
  • When used in combination with the Ion Total RNA-Seq Kit v2 , the Ion Xpress RNA-Seq Barcode 1-16 Kit enables users to pool up to 16 fragment libraries prior to template preparation and then conduct multiplexed sequencing analysis, simplifying the Ion semiconductor sequencing workflow for small and whole transcriptome RNA. (thermofisher.com)
  • RNA-seq reads aligning to the alternative exon body (white) or to splice junctions involving this exon support the inclusive isoform, whereas reads joining the two constitutive exons (black-gray exon junction) support the exclusive isoform. (nih.gov)
  • In order to understand the biosynthesis of secondary metabolites, Illumina-based deep transcriptome profiling and analysis was performed for four tissues (flower, bud, leaf, and root) of A. carmichaelii , resulting in 5.5 Gbps clean RNA-seq reads assembled into 128,183 unigenes. (mdpi.com)
  • The first step in the analysis process is to map the RNA-seq reads against the reference genome, which provides the location from which the reads originated. (umd.edu)
  • In order to cope with these problems effectively, I have developed new alignment algorithms and implemented them in TopHat2, a second version of TopHat (one of the first spliced aligners for RNA-seq reads). (umd.edu)
  • The new TopHat2 program can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length insertions and deletions with respect to the reference genome. (umd.edu)
  • The evaluated approaches included aligning the long reads to a graph created from short read alignments instead of the reference genome, which led to our final contribution: extending a co-linear chaining algorithm from between two sequences to between a sequence and a directed acyclic graph. (helsinki.fi)
  • Furthermore, by using long reads that did not require an assembly step, we were able to identify, in infected cells, diverse and novel HCoV-229E sg RNAs that remain to be characterized. (nanoporetech.com)
  • The resulting sequence reads are aligned with the reference genome or transcriptome, and classified as three types: exonic reads, junction reads and poly(A) end-reads. (rna-seqblog.com)
  • We demonstrate that long gDNA and cDNA reads have the potential to reveal long-range information not previously accessible using traditional sequencing methods. (frontiersin.org)
  • It is a curious fact to consider, that the ribosome is a large, mostly RNA-based molecular machine that 'reads' RNA, as one would expect a putative primordial self-replicating RNA or RNA-polymerase would do. (theleagueofreason.co.uk)
  • Sixty-one uniquely indexed cDNA libraries were pooled and sequenced on one lane on the Illumina Hiseq 2500. (labroots.com)
  • Illumina HiSeq2000 technology was utilized to perform deep sequencing of small RNAs (sRNAs) extracted from field-collected H. rufipes ticks in Gansu Province, China. (frontiersin.org)
  • By combining Illumina and Oxford Nanopore sequencing, we reconstructed a highly accurate consensus sequence of the human coronavirus (HCoV)-229E genome (27.3 kb). (nanoporetech.com)
  • The fast growing shoots mixed with six different heights and culms after leaf expansion of moso bamboo transcriptome were sequenced using the Illumina HiSeq™ 2000 sequencing platform, respectively. (rna-seqblog.com)
  • Our gene expression and single nucleotide variants analyses suggest that equivalent phenotypes are achieved without relying on a unique molecular event or fixed transcriptional programs. (pnas.org)
  • Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, Lonnerberg P, Linnarsson S (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. (springer.com)
  • The development of single cell RNA sequencing technologies has emerged as a powerful means of profiling the transcriptional behavior of single cells, leveraging the breadth of sequencing measurements to make inferences about cell type. (fluidigm.com)
  • RNA sequencing (RNA-seq) was used to identify the transcriptional profiling in control and rats injected with monocrotaline (MCT) for 1, 2, 3 and 4 weeks. (aging-us.com)
  • Despite these, only fewer studies have used RNA-seq to analyze the PAH transcriptional profiling. (aging-us.com)
  • RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop portal for understanding the expression, evolutionary trajectories and disease dynamics of RBPs in the context of post-transcriptional regulatory networks. (omictools.com)
  • RNA sequencing (RNA-seq) has become a standard procedure to investigate transcriptional changes between conditions and is routinely used in research and clinics. (ethz.ch)
  • This workflow is available for Human transcriptome analysis and can be easily adapted and used for other genomes. (nih.gov)
  • Several clinical and research projects at the Mayo Clinic have applied the MAP-RSeq workflow for RNA-Seq studies. (nih.gov)
  • We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. (biomedcentral.com)
  • Here, we present the open-source workflow for automated RNA-seq processing, integration and analysis (SePIA). (biomedcentral.com)
  • It does so by (1) expanding the utility of the pipeline engine Anduril [ 5 ] to include a bundle of RNA-seq tools and (2) by providing users with the framework in which to best utilize the tools: a set of executable but highly configurable pipeline scripts that, together, form one compendious workflow. (biomedcentral.com)
  • The method is evaluated with respect to accuracy, sensitivity to modified nucleotides in the template RNA, and phylogenetic usefulness, by examination of several 16S rRNAs whose gene sequences are known. (pnas.org)
  • The relative simplicity of this approach should facilitate a rapid expansion of the 16S rRNA sequence collection available for phylogenetic analyses. (pnas.org)
  • Phylogenetic analysis of 1234 and 1117 RNA-based and DNA-based clone sequences, respectively, showed that unclassified Bacteria were the most abundant sequences, representing on average 57% of all sequences analyzed. (epa.gov)
  • As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that were identified. (frontiersin.org)
  • Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. (jalview.org)
  • Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. (umd.edu)
  • Phylogenetic analysis based on 16S r-RNA sequence available from bacterial isolates was constructed. (nih.gov)
  • B. dermatitidis aligned most closely with the Ascomycetes Neurospora crassa and Podospora anserina , in agreement with previous phylogenetic analysis based on morphological criteria. (microbiologyresearch.org)
  • 16S ribosomal RNAs (rRNA) of 12 methylotrophic bacteria have been almost completely sequenced to establish their phylogenetic relationships. (microbiologyresearch.org)
  • A phylogenetic analysis of the purple photosynthetic bacteria. (microbiologyresearch.org)
  • The phylogenetic analysis of the PCR products revealed clustering of the sequences from patients and siblings into five major branches when the group A PCR primers were used. (diabetesjournals.org)
  • With the group B primers, the sequences from patients, siblings, and control subjects formed three major branches in the phylogenetic tree, where 6 of the 7 control subjects clustered together in a sub-branch of CBV-4/VD2921. (diabetesjournals.org)
  • Using a sequencing approach, we characterize several subgenomic viral RNAs from human nasopharyngeal specimens infected with the influenza A(H1N1)pdm09 virus. (asm.org)
  • Because of high mutation and recombination rates, genome replication by viral RNA-dependent RNA polymerases leads to populations of closely related viruses, so-called "quasispecies. (nanoporetech.com)
  • Here, we used a full-length, direct RNA sequencing (DRS) approach based on nanopores to characterize viral RNAs produced in cells infected with a human coronavirus. (nanoporetech.com)
  • Also, the DRS approach, which circumvents reverse transcription and amplification of RNA, allowed us to detect methylation sites in viral RNAs. (nanoporetech.com)
  • Our work paves the way for haplotype-based analyses of viral quasispecies by showing the feasibility of intra-sample haplotype separation. (nanoporetech.com)
  • Catara, Antonino 2015-10-01 00:00:00 Two representative isolates of a citrus tristeza virus population in Sicily, SG29 (aggressive) and Bau282 (mild), were sequenced via viral small RNAs (vsRNA) produced in budlings of sweet orange grafted on sour orange. (deepdyve.com)
  • The presence of EV-RNA in the blood cells of most newly diagnosed type 1 diabetic children supports the hypothesis that a viral infection acts as an exogenous factor. (diabetesjournals.org)
  • Since the advent of efficient cell-culture methods for HCV replication and, more recently, infection, there has been a need to efficiently sequence the viral RNA in these systems. (scripps.edu)
  • The adaptation of hepatitis C replicons to cell culture, which greatly increased their replication capacity, and the subsequent identification of viral point mutations responsible for this adaptation are prime examples of the type of phenotype-genotype connection that viral RNA sequencing methods can provide. (scripps.edu)
  • More recently, researchers have used similar sequencing methods to identify changes in replicons that represent viral adaptation to engineered mutations, adaptation to a variety of host cells, and viral evasion of antiviral compound susceptibility. (scripps.edu)
  • We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution. (biomedcentral.com)
  • Next, structural boundaries for the resulting loci were compared to 75,116 expressed structures defined by the RNA-seq tag alignments. (biomedcentral.com)
  • Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication. (jalview.org)
  • Sequence alignments represent a starting point for almost every sequence based analysis. (biomedcentral.com)
  • Since many downstream sequence analysis methods are based on the information represented by alignments, building correct alignments is challenging as both sequences and structures have to be taken into account. (biomedcentral.com)
  • Although the methods can be used also in the context of sequence and secondary structure alignments, they are not specifically designed to take advantage of the secondary structure information. (biomedcentral.com)
  • We examined the bacterial composition of chlorinated drinking water using 16S rRNA gene clone libraries derived from RNA and DNA extracted from twelve water samples collected in three different months (June, August, and September of 2007). (epa.gov)
  • The 16S r-RNA sequence of isolated bacterial strain PSTB-1 has shown more homology with reported strain Enterobacter cloacae sub sp. (nih.gov)
  • RNA Sequencing identifies bacterial feedback control mechanism to balance growth with making protein products. (rna-seqblog.com)
  • Previously bacterial short regulatory RNAs have been referred to as small RNAs, but they are not related to eukaryotic small RNAs. (wikipedia.org)
  • Spot 42 (spf) RNA is a regulatory non-coding bacterial small RNA encoded by the spf (spot forty-two) gene. (wikipedia.org)
  • During the course of the project, several methods for extracting the features from the spectra of biological sequences and several types of classifiers were tested. (psu.edu)
  • Results indicate that signal processing methods may be very suitable for analyzing biological sequences. (psu.edu)
  • Gene discovery methods (whether experimental or computational) typically assume that the target is a protein coding gene that produces a messenger RNA. (biomedcentral.com)
  • Based on that analysis, we proposed a method using the Negative Binomial model with Independent Dispersions (NBID) and compared its false discovery rate (FDR) control and power to those of other commonly used methods. (biomedcentral.com)
  • For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. (jalview.org)
  • This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. (biomedcentral.com)
  • This problem can be circumvented by RNA-seq technology, which provides hypothesis-free single nucleotide resolution of gene expression so that, theoretically, any expressed sequence can be detected and quantified, given appropriate computational/statistical methods and sufficient sequencing depth. (biomedcentral.com)
  • These methods are diverse and include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and metagenomic and 16S rRNA gene amplification analysis of microbial populations. (biomedcentral.com)
  • Our paper "Comparative Analysis of Single-Cell RNA Sequencing Methods" has been selected to be included in the annual Best of Molecular Cell collection 2018. (lmu.de)
  • About half of the methods showed a substantial excess of false discoveries, making these methods unreliable for DE analysis and jeopardizing reproducible science. (biomedcentral.com)
  • Methods - We determined expression levels with RNA sequencing. (uu.nl)
  • The methods we describe permit rapid and robust determination of HCV RNA sequences from cell culture. (scripps.edu)
  • The first sequencing of the human genome, performed using Fred Sanger's dideoxynucleotide-sequencing method, took 10 years, and cost an estimated US $3 billion 1 , 2 . (jove.com)
  • 2008. Accurate whole human genome sequencing using reversible terminator chemistry. (currentprotocols.com)
  • DECS (dsRNA isolation, exhaustive amplification, cloning, and sequencing) analysis has been shown to be capable of detecting unknown viruses. (mdpi.com)
  • Hashimshony T, Wagner F, Sher N, Yanai I (2012) CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. (springer.com)
  • Unlike traditional RNA-Seq techniques, long-read nanopore RNA sequencing allows accurate quantification and complete, full-length characterisation of native RNA or cDNA without fragmentation or amplification - streamlining analysis and removing potential sources of bias. (londoncallingconf.co.uk)
  • With no requirement for amplification or reverse transcription, nanopore sequencing allows direct identification of base modifications alongside the nucleotide sequence - no chemical or protocol adaptations are required. (londoncallingconf.co.uk)
  • We illustrate the implications of these issues on downstream analysis, such as somatic mutation and fusion calling and differential expression. (aacrjournals.org)
  • We further propose a novel differential expression analysis algorithm based on a negative binomial model with independent dispersions in each group (NBID). (biomedcentral.com)
  • A closely related application of scRNA-seq count modeling is single-cell differential expression (DE) analysis. (biomedcentral.com)
  • This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. (biomedcentral.com)
  • This is a fundamental challenge for differential expression (DE) analysis. (biomedcentral.com)
  • Researchers from University of Padova discuss results obtained on two real and one synthetic dataset, along with considerations about the perspectives of single-cell differential expression analysis. (rna-seqblog.com)
  • While standard differential expression (DE) analysis between two conditions has been extensively studied, and improved over the past deca des, RNA-seq time course (TC) DE analysis algorithms are still in their early stages. (ethz.ch)
  • In addition, gene ontology analysis indicated G-protein-coupled receptor had a much higher proportion of differential expression (22%) compared with other classes (∼ 5%), suggesting a potential role regulating subtle changes in cellular behavior. (bloodjournal.org)
  • We performed whole transcriptome sequencing analyses of metastatic human breast cancer cells subjected to the chemotherapeutic agent paclitaxel at the single-cell and population levels. (pnas.org)
  • We applied this pipeline to three different RNAseq strategies (whole-transcriptome, exome, and targeted RNA-seq) and performed an in-depth comparative analysis to investigate the implications of the choice of strategy on the downstream analysis and results. (aacrjournals.org)
  • Whole transcriptome analysis identifies mitochondrial dysfunction and myocardial inflammation, in part regulated by FOXO4 and E2F1 pathways, as early phenotypes preceding cardiac dysfunction and premature death. (ahajournals.org)
  • Whole transcriptome analysis is of growing importance in understanding how altered expression of genetic variants contributes to complex diseases such as cancer, diabetes, and heart disease. (thermofisher.com)
  • Applications covered in the study include de novo transcriptome assembly, expression profiling analysis, variant calling & transcriptome epigenetics, and small RNA sequencing. (openpr.com)
  • Only on a single-cell level, can you eliminate the biological noise that is inherent to standard gene expression analysis - providing you the insights needed for a deeper understanding of transcription dynamics. (qiagen.com)
  • We demonstrate in situ sequencing of point mutations and multiplexed gene expression profiling in human breast cancer tissue sections. (nih.gov)
  • Gene expression profiling of samples from biobanks requires a method that can be used with intact as well as partially degraded RNA. (springer.com)
  • In: Raghavachari N., Garcia-Reyero N. (eds) Gene Expression Analysis. (springer.com)
  • RNA sequencing (RNA-seq) has revolutionized the study of gene expression in animals, plants and microorganisms. (labroots.com)
  • In conclusion, 3'-RNA-seq is a cost effective method amenable to global gene expression studies at population-level, e.g., expression QTL (eQTL) mapping. (labroots.com)
  • Differential gene co‑expression analysis was performed using R/EBcoexpress package in R. DEGs in the gene co‑expression network were subjected to Gene Ontology analysis using the Database for Annotation, Visualization and Integration Discovery. (spandidos-publications.com)
  • Transcriptome was analyzed by RNA-Seq at 2 weeks, prior to expression of cardiac dysfunction, apoptosis, and fibrosis. (ahajournals.org)
  • We utilized weighted gene co-expression network analysis (WGCNA) to identify gene expression network modules associated with IA size and rupture. (ahajournals.org)
  • Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. (jove.com)
  • In addition, these developments have galvanized progress in many other areas such as gene-expression analysis through RNA-Sequencing (RNA-Seq), study of genome-wide epigenetic modifications, DNA-protein interactions, and screening for microbial diversity in human hosts. (jove.com)
  • Read counting and unique molecular identifier (UMI) counting are the principal gene expression quantification schemes used in single-cell RNA-sequencing (scRNA-seq) analysis. (biomedcentral.com)
  • First, with relatively high expression variability, most TE exons in mRNAs, especially those without exact counterparts in the UCSC RefSeq (Reference Sequence) gene tables, demonstrate low but still detectable expression levels in most tissue samples. (biomedcentral.com)
  • Affymetrix exon array and RNA-seq platforms, for generating large-scale exon-level gene expression profiling. (biomedcentral.com)
  • Following the advent of RNA-sequencing (RNA-seq) technologies, several statistical tools for differential gene expression (DGE) analysis have been introduced. (biomedcentral.com)
  • We hypothesize that subcellular fractions of RNA may provide a more accurate picture of gene expression. (biomedcentral.com)
  • Further analysis revealed impaired expression of cholinergic receptors, adrenergic receptors including alpha1, beta1 and beta2 receptor, and dysregulated expression of γ-aminobutyric acid receptors. (aging-us.com)
  • Nonresponders and responders were distinguished by distinct pretraining molecular (DNA methylation, RNA expression) patterns in muscle tissue, as well as in HSkMCs. (diabetesjournals.org)
  • MicroRNAs (miRNA) are 19- to 23-nucleotide (nt) RNAs that regulate gene expression ( 3-5 ). (aacrjournals.org)
  • Here, we surveyed by barcoded Solexa sequencing 185 breast specimens, including 11 normal breast, 17 ductal carcinoma in situ (DCIS), 151 invasive carcinomas [including 126 invasive ductal carcinomas (IDC)], and 6 ductal cell lines and obtained expression levels based on sequence read number. (aacrjournals.org)
  • High throughout RNA sequencing allows genome-wide investigation of gene expression and regulation. (tuftsctsi.org)
  • Low input amounts combined with rapid, streamlined workflows enable highly sensitive gene expression analysis, even from single cells. (londoncallingconf.co.uk)
  • Analysis of genome-wide differential RNA expression provides researchers with greater insights into biological pathways and molecular mechanisms that regulate cell fate, development, and disease progression. (thermofisher.com)
  • Transcriptome analysis of CD34 + -enriched human CB populations revealed induction of endothelial protein C receptor (EPCR) gene expression on UM171 treatment. (bloodjournal.org)
  • By using this technique, it is possible to discriminate small RNAs from the larger RNA family to better understand their functions in the cell and in gene expression. (wikipedia.org)
  • Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. (biomedcentral.com)
  • Our new solutions for single-cell RNA-seq deliver a deeper understanding of the transcriptome, providing new biological insights. (qiagen.com)
  • Here, we studied drug resistance dynamics in a model of tolerance with a metastatic breast cancer cell line by leveraging the power of single-cell RNA-Seq technology. (pnas.org)
  • Thus, single-cell analyses reveal the dynamics of the stress response in terms of cell-specific RNA variants driving heterogeneity, the survival of a minority population through generation of specific RNA variants, and the efficient reconversion of stress-tolerant cells back to normalcy. (pnas.org)
  • Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X, Lao K, Surani MA (2010) Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. (springer.com)
  • Our results provide guidelines for selecting sequencing depth and complexity thresholds for single cell RNA sequencing. (fluidigm.com)
  • SCOPIT: sample size calculations for single-cell sequencing experiments. (viictr.org)
  • Highly multiplexed single-cell approaches including single-cell RNA sequencing (scRNAseq) have emerged as resources to help answer these questions. (ntno.org)
  • Single-cell RNA-seq (scRNAseq) is a powerful tool to study heterogeneity of cells. (aston.ac.uk)
  • We have compared the nucleotide sequences of the small RNA segments of two attenuated, low-passage variants of the PIC virus Munchique strain (CoAn 4763) and two virulent, high-passage derivatives. (ajtmh.org)
  • Evolution of nucleotide sequences. (microbiologyresearch.org)
  • By looking at this single molecular machine and analyzing nucleotide sequences in detail, we are quite possibly looking at what used to be almost the entire genome of one of the very first stages of life in the RNA world. (theleagueofreason.co.uk)
  • Given an input pairwise sequence alignment (e.g. from a BLASTN comparison of two related genomes) we classify the alignment into the coding, RNA, or null class according to the posterior probability of each class. (biomedcentral.com)
  • First, any RNA-seq alignment program must be able to handle gapped alignment (or spliced alignment) with very large gaps due to introns, typically from 50-100,000 bases in mammalian genomes. (umd.edu)
  • Sequence analyses of RNA virus genomes remain challenging owing to the exceptional genetic plasticity of these viruses. (nanoporetech.com)
  • Standard (short-read) sequencing technologies are ill-suited to reconstruct large numbers of full-length haplotypes of (1) RNA virus genomes and (2) subgenome-length (sg) RNAs composed of noncontiguous genome regions. (nanoporetech.com)
  • Little knowledge about long non-coding RNAs(lncRNAs) in nasopharyngeal carcinoma (NPC) has been acquired. (jcancer.org)
  • Long non-coding RNAs (lncRNAs) are typically expressed at low levels and are inherently highly variable. (biomedcentral.com)
  • Experience in pathway analyses or network modeling will be considered as an advantage. (bioinformatics.org)
  • Pathway analysis identified down-regulation of mitochondrial OXPHOS and upregulation of the inflammatory pathways in the Lmna-/- heart. (ahajournals.org)
  • Pathway analysis was used to identify enriched pathways. (uu.nl)
  • Here, we describe a model case in which we efficiently detected the presumed genome sequence of Blueberry shoestring virus (BSSV), a member of the genus Sobemovirus , which has not so far been reported. (mdpi.com)
  • 2016. The mechanism of RNA 5′ capping with NAD+, NADH, and desphospho-CoA . (rutgers.edu)
  • 2016. Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. . (rutgers.edu)
  • RNA was isolated from peripheral blood mononuclear cells and EV-RNA detected by RT-PCR. (diabetesjournals.org)
  • While there are many resources readily available to effectively perform RNA-seq experiments, optimal protocols and analysis tools for the cancer domain remain to be developed. (aacrjournals.org)
  • We describe a protocol for C. elegans researchers to perform RNA-Seq experiments, access and process the dataset using Galaxy and obtain meaningful biological information from the gene lists using DAVID. (jove.com)
  • Based on technology, the market is classified into sequencing by synthesis (SBS), ion semiconductor sequencing, single-molecule real-time (SMRT) sequencing, and nanopore sequencing. (openpr.com)
  • Once small RNAs have been isolated, it is important to quantify them and to evaluate the quality of the purification. (wikipedia.org)
  • It was discovered by polyacrylamide gel electrophoresis and 2-D fingerprinting in an attempt to study the accumulation of small RNAs in E. coli during amino acid starvation. (wikipedia.org)
  • We have implemented this approach as a program, QRNA, which we consider to be a prototype structural noncoding RNA genefinder. (biomedcentral.com)
  • The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. (biomedcentral.com)
  • Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. (biomedcentral.com)
  • Our analysis has characterized the technical features of the different library preparations, providing a necessary understanding of the costs and benefits of each method and the potential effects on the downstream analyses. (aacrjournals.org)
  • These new capabilities will contribute to improvements in the quality of downstream analysis. (umd.edu)
  • The key idea is to test the pattern of substitutions observed in a pairwise alignment of two homologous sequences. (biomedcentral.com)
  • In contrast to DNA sequence alignment, RNA-seq mapping algorithms have two additional challenges. (umd.edu)
  • Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. (jalview.org)
  • Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview . (jalview.org)
  • A common task is to manualy check and improve the alignment before using it for further analysis. (biomedcentral.com)
  • A different approach of visualizing RNA alignment information is given with the S2S framework [ 14 ], which interconnects an RNA sequence alignment with a consensus secondary and the 3D tertiary structure visualization. (biomedcentral.com)
  • While this approach can help to get a good understanding of the common structural information within the RNA sequence alignment, it can not handle individual secondary structure information. (biomedcentral.com)
  • The sRNA deep-sequencing approach used in this analysis provides an intuitive method to survey micropathogen prevalence in ticks and other vector species. (frontiersin.org)
  • 11) has been used to transcribe complementary DNA probes from the four major RNA species of cucumber mosaic virus (RNAs 1 - 4 in order of decreasing molecular weight). (eurekamag.com)
  • The group I methylotrophs, Methylophilus methylotrophus strain AS1 and methylotrophic species DM11, which do not utilize methane, are similar in 16S rRNA sequence to bacteria in the β -subdivision. (microbiologyresearch.org)
  • Sequence analysis of RNA species synthesized by Q beta replicase without template. (mpg.de)
  • Spot42 was first described in 1973 as an unstable RNA species of 109 nucleotides in Escherichia coli. (wikipedia.org)
  • By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily. (biomedcentral.com)
  • Direct RNA sequencing also enables the identification of base modifications alongside nucleotide sequence. (londoncallingconf.co.uk)
  • The report offers a quantitative analysis from 2017 to 2023, which is expected to enable the stakeholders to capitalize on prevailing market opportunities. (openpr.com)
  • 2017. Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence . (rutgers.edu)
  • We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (umd.edu)
  • dsRNAs were isolated from BSSV-infected blueberry plants using the dsRNA-binding protein, reverse-transcribed, amplified, and sequenced using NGS. (mdpi.com)
  • A recombinant protein encoded by the putative coat protein gene was bound by the BSSV-antibody, indicating that the candidate sequence was that of BSSV itself. (mdpi.com)
  • Suitable, asymmetrical restriction sites in the construct allow for the insertion of sequences of interest, e. g. protein binding sites. (degruyter.com)
  • Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. (jalview.org)
  • Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. (jalview.org)
  • Analysis of the kinetics of hybridization of these probes in homologous and heterologous complementary DNA-RNA hybridization reactions has shown that the sequence of the smallest RNA (RNA 4), which contains the coat protein gene, is present within RNA 3. (eurekamag.com)
  • Despite LncRNA-protein-based relationship technology as RNA Immunoprecipitation (RIP)-chip and RIP-sequencing, its antibody specificity made the research focus on one point. (jcancer.org)
  • It is exciting to see how much one can learn from a few gene or protein sequences. (coursera.org)
  • We can use similar sequences to infer homology, which is the primary predictor of gene or protein function. (coursera.org)
  • X chromosome inactivation by Xist RNA), epigenetics modifications, protein stability and transport. (wikipedia.org)
  • Analysis and design of RNA sequencing experiments for identifying isoform regulation. (nih.gov)
  • Overall, we anticipate that this article will provide information to C. elegans researchers undertaking RNA-Seq experiments for the first time as well as frequent users running a small number of samples. (jove.com)
  • As if that wasn't enough, additional metabolic and replication-related enzymes and ribozymes are encoded in overlapping readingframes in ribosomal RNA. (theleagueofreason.co.uk)
  • This need is especially urgent in light of the error-prone nature of HCV RNA replication, which leads to a variety of interesting mutations. (scripps.edu)
  • Cieslik M, Chugh R, Wu Y-M et al (2015) The use of exome capture RNA-Seq for highly degraded RNA with application to clinical cancer sequencing. (springer.com)
  • therefore, transcriptome analysis across multiple tissues is an attractive method to identify the molecular components involved for further functional characterization. (mdpi.com)
  • When performed on statistically meaningful sample group sizes, unbiased global profiling analyses utilizing peripheral tissues are critical for the discovery and validation of FRDA disease biomarkers. (curefa.org)
  • The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues. (viictr.org)
  • We profiled miRNAs from 11 normal breast tissues, 17 noninvasive, 151 invasive breast carcinomas, and 6 cell lines by in-house-developed barcoded Solexa sequencing. (aacrjournals.org)
  • Here, we apply the first study of using long read sequencing with targeted capture of both the gDNA and cDNA of the SNCA gene in brain tissues of PD, DLB, and control samples using the PacBio Sequel system. (frontiersin.org)
  • Reverse transcription (RT)-PCR primer sets based on sequences from this contig enabled the detection of BSSV in all BSSV-infected plants tested but not in healthy controls. (mdpi.com)
  • Recently, RNA-seq has emerged as an alternative to microarray, because of its accuracy, sensibility, larger dynamic detection range and higher reproducibility than microarray [ 4 , 5 ]. (aging-us.com)