The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
Chronic endemic respiratory disease of dairy calves and an important component of bovine respiratory disease complex. It primarily affects calves up to six months of age and the etiology is multifactorial. Stress plus a primary viral infection is followed by a secondary bacterial infection. The latter is most commonly associated with PASTEURELLA MULTOCIDA producing a purulent BRONCHOPNEUMONIA. Sometimes present are MANNHEIMIA HAEMOLYTICA; HAEMOPHILUS SOMNUS and mycoplasma species.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
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.
Sets of structured vocabularies used for describing and categorizing genes, and gene products by their molecular function, involvement in biological processes, and cellular location. These vocabularies and their associations to genes and gene products (Gene Ontology annotations) are generated and curated by the Gene Ontology Consortium.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The functional hereditary units of PLANTS.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
Databases devoted to knowledge about specific genes and gene products.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.
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.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The protein complement of an organism coded for by its genome.
Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.
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.
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.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The unfavorable effect of environmental factors (stressors) on the physiological functions of an organism. Prolonged unresolved physiological stress can affect HOMEOSTASIS of the organism, and may lead to damaging or pathological conditions.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990)
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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
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.
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.
Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)
The relationships of groups of organisms as reflected by their genetic makeup.
A disease caused by any of a number of species of protozoa in the genus LEISHMANIA. There are four major clinical types of this infection: cutaneous (Old and New World) (LEISHMANIASIS, CUTANEOUS), diffuse cutaneous (LEISHMANIASIS, DIFFUSE CUTANEOUS), mucocutaneous (LEISHMANIASIS, MUCOCUTANEOUS), and visceral (LEISHMANIASIS, VISCERAL).
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 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)
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
The different gene transcripts generated from a single gene by RNA EDITING or ALTERNATIVE SPLICING of RNA PRECURSORS.
The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.
Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
The reproductive organs of plants.
Sets of enzymatic reactions occurring in organisms and that form biochemicals by making new covalent bonds.
The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
A plant genus of the family FABACEAE known for the edible beans.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
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.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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)
Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
Any method used for determining the location of and relative distances between genes on a chromosome.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Sequential operating programs and data which instruct the functioning of a digital computer.
In eukaryotes, a genetic unit consisting of a noncontiguous group of genes under the control of a single regulator gene. In bacteria, regulons are global regulatory systems involved in the interplay of pleiotropic regulatory domains and consist of several OPERONS.
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.
Peptides composed of two amino acid units.
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.
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
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).
A species of ciliated PARAMECIUM possessing two micronuclei.
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.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
A very toxic anthracycline-type antineoplastic related to DAUNORUBICIN, obtained from Actinomadura carminata.
Short RNA, about 200 base pairs in length or shorter, that does not code for protein.
Prolonged dry periods in natural climate cycle. They are slow-onset phenomena caused by rainfall deficit combined with other predisposing factors.
A type of male infertility in which no germ cells are visible in any of the biopsied SEMINIFEROUS TUBULES (type I) or in which germ cells are present in a minority of tubules (type II). Clinical features include AZOOSPERMIA, normal VIRILIZATION, and normal chromosomal complement.
The measurement of visualization by radiation of any organ after a radionuclide has been injected into its blood supply. It is used to diagnose heart, liver, lung, and other diseases and to measure the function of those organs, except renography, for which RADIOISOTOPE RENOGRAPHY is available.
The genetic complement of a helminth (HELMINTHS) as represented in its DNA.
Drugs that inhibit ADENOSINE DEAMINASE activity.
The original member of the family of endothelial cell growth factors referred to as VASCULAR ENDOTHELIAL GROWTH FACTORS. Vascular endothelial growth factor-A was originally isolated from tumor cells and referred to as "tumor angiogenesis factor" and "vascular permeability factor". Although expressed at high levels in certain tumor-derived cells it is produced by a wide variety of cell types. In addition to stimulating vascular growth and vascular permeability it may play a role in stimulating VASODILATION via NITRIC OXIDE-dependent pathways. Alternative splicing of the mRNA for vascular endothelial growth factor A results in several isoforms of the protein being produced.
Techniques using a laser to cut away and harvest a specific cell or cluster of cells from a tissue section while viewing it under the microscope.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
Degree of saltiness, which is largely the OSMOLAR CONCENTRATION of SODIUM CHLORIDE plus any other SALTS present. It is an ecological factor of considerable importance, influencing the types of organisms that live in an ENVIRONMENT.
Proteins found in any species of insect.
The functional hereditary units of INSECTS.
The genetic complement of a BACTERIA as represented in its DNA.
The complete gene complement contained in a set of chromosomes in a fungus.
A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
A large order of insects characterized by having the mouth parts adapted to piercing or sucking. It is comprised of four suborders: HETEROPTERA, Auchenorrhyncha, Sternorrhyncha, and Coleorrhyncha.
The GENETIC RECOMBINATION of the parts of two or more GENES resulting in a gene with different or additional regulatory regions, or a new chimeric gene product. ONCOGENE FUSION includes an ONCOGENE as at least one of the fusion partners and such gene fusions are often detected in neoplastic cells and are transcribed into ONCOGENE FUSION PROTEINS. ARTIFICIAL GENE FUSION is carried out in vitro by RECOMBINANT DNA technology.
Antihistamine drug now withdrawn from the market in many countries because of rare but potentially fatal side effects.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.
The fruiting 'heads' or 'caps' of FUNGI, which as a food item are familiarly known as MUSHROOMS, that contain the FUNGAL SPORES.
A subset of various vascular plants (also known as the Tracheophyta) which include seed-bearing and non seed-bearing species.
Any of the hormones produced naturally in plants and active in controlling growth and other functions. There are three primary classes: auxins, cytokinins, and gibberellins.
A plant genus of the family SALICACEAE. Balm of Gilead is a common name used for P. candicans, or P. gileadensis, or P. jackii, and sometimes also used for ABIES BALSAMEA or for COMMIPHORA.
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
Very young plant after GERMINATION of SEEDS.
Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The encapsulated embryos of flowering plants. They are used as is or for animal feed because of the high content of concentrated nutrients like starches, proteins, and fats. Rapeseed, cottonseed, and sunflower seed are also produced for the oils (fats) they yield.
Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.
A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
Proteins obtained from species of fish (FISHES).
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).
Deoxyribonucleic acid that makes up the genetic material of plants.
Cellular processes in biosynthesis (anabolism) and degradation (catabolism) of CARBOHYDRATES.
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
The continuous sequence of changes undergone by living organisms during the post-embryonic developmental process, such as metamorphosis in insects and amphibians. This includes the developmental stages of apicomplexans such as the malarial parasite, PLASMODIUM FALCIPARUM.
A plant genus of the family FABACEAE that is used for food in NIGERIA.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.
The joining of RNA from two different genes. One type of trans-splicing is the "spliced leader" type (primarily found in protozoans such as trypanosomes and in lower invertebrates such as nematodes) which results in the addition of a capped, noncoding, spliced leader sequence to the 5' end of mRNAs. Another type of trans-splicing is the "discontinuous group II introns" type (found in plant/algal chloroplasts and plant mitochondria) which results in the joining of two independently transcribed coding sequences. Both are mechanistically similar to conventional nuclear pre-mRNA cis-splicing. Mammalian cells are also capable of trans-splicing.
Heat- and storage-stable plasma protein that is activated by tissue thromboplastin to form factor VIIa in the extrinsic pathway of blood coagulation. The activated form then catalyzes the activation of factor X to factor Xa.
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
The capacity of an organism to defend itself against pathological processes or the agents of those processes. This most often involves innate immunity whereby the organism responds to pathogens in a generic way. The term disease resistance is used most frequently when referring to plants.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Knobbed structures formed from and attached to plant roots, especially of LEGUMES, which result from symbiotic infection by nitrogen fixing bacteria such as RHIZOBIUM or FRANKIA. Root nodules are structures related to MYCORRHIZAE formed by symbiotic associations with fungi.
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 body of a fungus which is made up of HYPHAE.
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.
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.
Genotypic differences observed among individuals in a population.
The functional hereditary units of BACTERIA.
Threatened or actual attempt to harm others at place of employment.
Biological activities and function of the whole organism in human, animal, microorgansims, and plants, and of the biosphere.
A species of the family Ranidae which occurs primarily in the eastern half of the United States and Canada. Two subspecies exist, commonly referred to as green frog (R. c. melanota) and bronze frog (R. c. clamitans).
Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
A cell line derived from cultured tumor cells.
Adaptation to a new environment or to a change in the old.
Spontaneous or near spontaneous bleeding caused by a defect in clotting mechanisms (BLOOD COAGULATION DISORDERS) or another abnormality causing a structural flaw in the blood vessels (HEMOSTATIC DISORDERS).
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
An element with the atomic symbol N, atomic number 7, and atomic weight [14.00643; 14.00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth's atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells.
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 Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.
Elements of limited time intervals, contributing to particular results or situations.
A plant species of the family SOLANACEAE, native of South America, widely cultivated for their edible, fleshy, usually red fruit.
The performance of dissections with the aid of a microscope.
A mitosporic fungal genus. P. brasiliensis (previously Blastomyces brasiliensis) is the etiologic agent of PARACOCCIDIOIDOMYCOSIS.
Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.
A plant genus of the family POACEAE widely cultivated in the tropics for the sweet cane that is processed into sugar.
Paired sense organs connected to the anterior segments of ARTHROPODS that help them navigate through the environment.
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.
Wormlike or grublike stage, following the egg in the life cycle of insects, worms, and other metamorphosing animals.
A plant genus in the family PINACEAE, order Pinales, class Pinopsida, division Coniferophyta. They are evergreen trees mainly in temperate climates.
A plant genus of the family Plantaginaceae. Members contain scrosides (CINNAMATES) and phenylethanoid glycoside. P. kurrooa is the source of picroliv (a purified iridoid glycoside fraction from the roots having hepatoprotective, anti-inflammatory and antioxidant properties).
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
A plant genus of the family ELAEAGNACEAE. Linoleic (18:2n-6) and alpha-linolenic acids (18:3n-3) comprised about 70% of seed oil fatty acids. This is unrelated to 'artificial sea buckthorn oil'. This genus does not belong to the buckthorn family (RHAMNACEAE).
The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.
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.
Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.
A plant species of the genus CITRUS, family RUTACEAE that provides the familiar orange fruit which is also a source of orange oil.
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.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.
A plant genus of the family TAXODIACEAE. Members contain DITERPENES.
A plant genus of the family DENNSTAEDTIACEAE. Members contain ptaquiloside, braxin A1, and braxin B. The name is similar to brake fern (PTERIS).
A plant genus in the family VITACEAE, order Rhamnales, subclass Rosidae. It is a woody vine cultivated worldwide. It is best known for grapes, the edible fruit and used to make WINE and raisins.
The genetic complement of an insect (INSECTS) as represented in its DNA.
An organophosphate cholinesterase inhibitor that is used as a pesticide.
Eighteen-carbon cyclopentyl polyunsaturated fatty acids derived from ALPHA-LINOLENIC ACID via an oxidative pathway analogous to the EICOSANOIDS in animals. Biosynthesis is inhibited by SALICYLATES. A key member, jasmonic acid of PLANTS, plays a similar role to ARACHIDONIC ACID in animals.
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.
Morphological and physiological development of EMBRYOS.
Ratio of output to effort, or the ratio of effort produced to energy expended.
A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.
Parts of plants that usually grow vertically upwards towards the light and support the leaves, buds, and reproductive structures. (From Concise Dictionary of Biology, 1990)
A large family of mollusks in the class BIVALVIA, known commonly as scallops. They possess flat, almost circular shells and are found in all seas from shallow water to great depths.
A plant species of the family FABACEAE used to study GENETICS because it is DIPLOID, self fertile, has a small genome, and short generation time.
An absence of warmth or heat or a temperature notably below an accustomed norm.
Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.
A plant genus of the family BRASSICACEAE known for its peppery red root.
A plant genus of the family EUPHORBIACEAE, order Euphorbiales, subclass Rosidae. Commercial natural RUBBER is mainly obtained from Hevea brasiliensis but also from some other plants.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
Genetic loci associated with a QUANTITATIVE TRAIT.
A plant genus in the family PINACEAE, order Pinales, class Pinopsida, division Coniferophyta. They are coniferous evergreen trees with long, flat, spirally arranged needles that grow directly from the branch.
A genus of basidiomyceteous fungi in the family POLYPORACEAE. The species all contain bright orange, bracket-like fruiting bodies.
The relationship between an invertebrate and another organism (the host), one of which lives at the expense of the other. Traditionally excluded from definition of parasites are pathogenic BACTERIA; FUNGI; VIRUSES; and PLANTS; though they may live parasitically.
Derivatives of ethylene, a simple organic gas of biological origin with many industrial and biological use.
A plant genus of the family POACEAE. Young shoots are eaten in Asian foods while the stiff mature stems are used for construction of many things. The common name of bamboo is also used for other genera of Poaceae including Phyllostachys, SASA, and Dendrocalamus.
A genus of plant viruses in the family CLOSTEROVIRIDAE. Transmission is by whiteflies. Lettuce infectious yellows virus is the type species.
Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.
The fertilizing element of plants that contains the male GAMETOPHYTES.
A nonmetallic element with atomic symbol C, atomic number 6, and atomic weight [12.0096; 12.0116]. It may occur as several different allotropes including DIAMOND; CHARCOAL; and GRAPHITE; and as SOOT from incompletely burned fuel.
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.
The outermost layer of a cell in most PLANTS; BACTERIA; FUNGI; and ALGAE. The cell wall is usually a rigid structure that lies external to the CELL MEMBRANE, and provides a protective barrier against physical or chemical agents.
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.
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide using energy obtained from light rather than from the oxidation of chemical compounds. Photosynthesis comprises two separate processes: the light reactions and the dark reactions. In higher plants; GREEN ALGAE; and CYANOBACTERIA; NADPH and ATP formed by the light reactions drive the dark reactions which result in the fixation of carbon dioxide. (from Oxford Dictionary of Biochemistry and Molecular Biology, 2001)
Plant tissue that carries water up the root and stem. Xylem cell walls derive most of their strength from LIGNIN. The vessels are similar to PHLOEM sieve tubes but lack companion cells and do not have perforated sides and pores.
A group of alicyclic hydrocarbons with the general formula R-C5H9.
The most abundant natural aromatic organic polymer found in all vascular plants. Lignin together with cellulose and hemicellulose are the major cell wall components of the fibers of all wood and grass species. Lignin is composed of coniferyl, p-coumaryl, and sinapyl alcohols in varying ratios in different plant species. (From Merck Index, 11th ed)
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.
Proteins synthesized by organisms belonging to the phylum ARTHROPODA. Included in this heading are proteins from the subdivisions ARACHNIDA; CRUSTACEA; and HORSESHOE CRABS. Note that a separate heading for INSECT PROTEINS is listed under this heading.
Paired respiratory organs of fishes and some amphibians that are analogous to lungs. They are richly supplied with blood vessels by which oxygen and carbon dioxide are exchanged directly with the environment.
Inorganic compounds that include a positively charged tetrahedral nitrogen (ammonium ion) as part of their structure. This class of compounds includes a broad variety of simple ammonium salts and derivatives.

Effects of basic fibroblast growth factor on the expressions of angiogenic gene profile and cyclooxygenase-2 in brain microvascular endothelial cells. (1/4463)

The present study aimed to investigate the effects of basic fibroblast growth factor (bFGF) on the expressions of angioge-nesis-related genes in a mouse brain microvascular endothelial cell line, namely bEnd.3, using cDNA microarray. The effects of bFGF (10 ng/ml) on mRNA and protein expressions of cyclooxygenase-2 (COX-2), an angiogenesis bystander molecule, were further investigated. cDNA microarray was employed to study the effects of bFGF on the expressions of angiogenic genes in a high throughput pattern. RT-PCR was used to study the effect of bFGF on COX-2 mRNA expression. Western blot and immunocytochemistry were utilized to study the effect of bFGF on COX-2 protein expression. The results showed that, 2 h after bFGF treatment, pro-angiogenic genes (Adamts1, MMP-9, Ang-1, PDGF B, G-CSF, FGF16, IGF-1, etc.) were significantly upregulated, whereas anti-angiogenic genes (TIMP-2, TSP-3, etc.) were significantly downregulated. The bystander molecule in angiogenic pathway COX-2 mRNA and protein expressions were significantly upregulated after bFGF treatment. It is suggested that triggering angiogensis switch through upregulating pro-angiogenic gene and downregulating anti-angiogenic gene expression is one of the major mechanisms of bFGF-induced angiogenesis. The expression change of COX-2, as a bystander molecule, was observed after bFGF treatment in bEnd.3 cells and the significance was discussed.  (+info)

Stress-dependent coordination of transcriptome and translatome in yeast. (2/4463)

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Variation in dehydration tolerance, ABA sensitivity and related gene expression patterns in D-genome progenitor and synthetic hexaploid wheat lines. (3/4463)

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Identification and classification of small RNAs in transcriptome sequence data. (4/4463)

Current methods for high throughput sequencing (HTS) for the first time offer the opportunity to investigate the entire transcriptome in an essentially unbiased way. In many species, small non-coding RNAs with specific secondary structures constitute a significant part of the transcriptome. Some of these RNA classes, in particular microRNAs and snoRNAs, undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome specific patterns of short reads can be observed. These read patterns seem to reflect the processing and thus are specific for the RNA transcripts of which they are derived from. We explore here the potential of short read sequence data in the classification and identification of non-coding RNAs.  (+info)

The transcriptome of human monocyte subsets begins to emerge. (5/4463)

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A focus on natural variation for abiotic constraints response in the model species Arabidopsis thaliana. (6/4463)

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A marginal mixture model for selecting differentially expressed genes across two types of tissue samples. (7/4463)

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Use of type I interferon-inducible mRNAs as pharmacodynamic markers and potential diagnostic markers in trials with sifalimumab, an anti-IFNalpha antibody, in systemic lupus erythematosus. (8/4463)

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TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published
Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Due to the rapid increase in throughputs and decrease in costs of next generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Here, researchers from BGI Shenzhen, present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. They evaluated its performance on transcriptome datasets from rice and mouse. Using as their benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), they assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. AVAILABILITY
While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. We develop a divide-and-conquer strategy that allows these algorithms to be utilized, by subdividing a large RNA-Seq data set into small libraries. Each individual library is assembled independently by an existing algorithm, and a merging algorithm is developed to combine these assemblies by picking a subset of high quality transcripts to form a large transcriptome. When compared to existing algorithms that return a single assembly directly, this strategy achieves comparable or increased accuracy as memory-efficient algorithms that can be used to process a large amount of ...
RNA-seq enables gene expression profiling in selected spatiotemporal windows and yields massive sequence information with relatively low cost and time investment, even for non-model species. However, there remains a large room for optimizing its workflow, in order to take full advantage of continuously developing sequencing capacity. Transcriptome sequencing for three embryonic stages of Madagascar ground gecko (Paroedura picta) was performed with the Illumina platform. The output reads were assembled de novo for reconstructing transcript sequences. In order to evaluate the completeness of transcriptome assemblies, we prepared a reference gene set consisting of vertebrate one-to-one orthologs. To take advantage of increased read length of |150 nt, we demonstrated shortened RNA fragmentation time, which resulted in a dramatic shift of insert size distribution. To evaluate products of multiple de novo assembly runs incorporating reads with different RNA sources, read lengths, and insert sizes, we
Nitraria sibirica Pall., a typical halophyte of great ecological value, is widely distributed in desert, saline, and coastal saline-alkali environments. Consequently, researching the salt tolerance mechanism of N. sibirica Pall. has great significance to the cultivation and utilization of salt-tolerant plants. In this research, RNA-seq, digital gene expression (DGE), and high flux element analysis technologies were used to investigate the molecular and physiological mechanisms related to salt tolerance of N. sibirica Pall. Integrative analysis and de novo transcriptome assembly generated 137,421 unigenes. In total, 58,340 and 34,033 unigenes were annotated with gene ontology (GO) terms and mapped in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. Three differentially expressed genes (DEGs) libraries were subsequently constructed from the leaves of N. sibirica Pall. seedlings under different treatments: control (CK), light short-term salt stress (CL2), and heavy long-term salt
Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here the authors present Trinity and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. This approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome. Trinity is
Niamh Biddulph said:Graduating is the start of life where anything is possible. I can make my own decisions and follow my dreams. Trinity gave me that. I never expected I could be a Trinity graduate, its great to celebrate something I thought was never going to be an option for me. Mark Hogan said: You have to show loyalty and respect and earn your place in Trinity College and never give up on your dream. If you work very hard in Trinity College you can be more independent and responsible by doing your work and bringing it in on time. If you do your work properly you will achieve success and complete all the modules in Trinity College. Everyone has to be equal. Do not compare yourself to others. Everybody has their own opinions and rights which should be respected. I put my mind in to doing my work and I never give up on my dreams. Graduating is very important to all of us because we are all together in one happy class and its all thanks to Trinity College and all the staff working there. ...
Variants were called using a pipeline based on GATK 2.8.1 (2.5.2 for steps before genotyping) [50], roughly following GATK best practices [94, 95]. GATK is, however, primarily designed for low coverage genomic re-sequencing of mammalian model organisms. Adaptations and parameter choices are needed to apply it to RNA-Seq reads (with their highly variable coverage reaching extraordinary levels for the highest genes) and de novo assembled contigs in a non-model organism such as oak, not only for computational considerations but also quality of output. The pipeline begins with the final draft oak transcriptome contigs as reference and the Illumina RTA PF = 1 paired-end 100 + 100 base reads tagged by individual with per-base RTA Phred-scale quality scores (with Illumina EAMSS quality score adjustments applied) as reads.. Reads were aligned to the reference with Bowtie 2.1.0 [87] as paired ends (−q --very-sensitive-local --n-ceil L,2,0 --dpad 12 --gbar 5 --score-min L,102,0 --minins 75 --maxins 500 ...
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
I previously created a C.bairdi de novo transcriptome assembly v4.0 with Trinity from all our C.bairdi RNAseq reads which had BLASTx matches to the C.opilio genome and decided to assess its
When my daughter, Trinity, was 5 yrs old, we took her in to our family physician for a normal school physical. The doctor did a Scoliosis check on her and suggested that we have some X-rays done as more of a precaution than anything. To this point, Trinity had never complained of any pain, we had never seen any signs of something wrong.... After her X-rays they showed them to me, and I almost collapsed at the picture. It was literally an S. We were blessed to find our orthopedic surgeon. He measured her the 1st time, and both of curves came out to about 50 degrees each. We tried having custom braces made, but none helped. On Valentines Day, 2012, at the age of 6 yrs old, Trinity had her 1st surgery. The doctor put rods in her back. Her curves had measured 62 degrees each. She was so upset about missing her first school Valentines Day party that she asked if she could have pink hair, and all the nurses & doctors loved it!. Over the years, Trinity has had 4 adjustment surgeries. She never let ...
Transcriptomic analysis promises to have a real impact on the field of transplantation, particularly in the improvement of post-transplant immune surveillance and the improvement of patient diagnoses during their follow-up. We expect a lot from transcriptomic analysis. If viewed as a companion to histology, it could support complex cases and shed light on the type of diagnosis to be made and therefore the treatment to be followed, concludes professor Jean-Paul Duong Van Huyen. In the longer term, we could even imagine that the transcriptomic signature could be one of the molecular parameters systematically used. In fact, testing the validity and use of molecular analyses in transplantation is one of the objectives of the pathologists and bioinformaticians in the Paris Transplant Groups research group. ...
TY - JOUR. T1 - An integrative transcriptomic approach to identify depot differences in genes and microRNAs in adipose tissues from high fat fed mice.. AU - Wijayatunga, Nadeeja. AU - Pahlavani, Mandana. AU - Kalupahana, N S. AU - Kottapalli, Kameswara. AU - Gunaratne, P H. AU - Coarfa, C. AU - Ramalingam, Latha. AU - Moustaid-Moussa, Naima. PY - 2018/1/13. Y1 - 2018/1/13. M3 - Article. SP - 9246. EP - 9261. JO - Default journal. JF - Default journal. ER - ...
We are offering up to 12 transcriptome sequencing grants in partnership with our Certified Service Providers. The winners projects will be completed by our CSP co-sponsors. Each grant will include the processing of up to 24 samples using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit on the Ion Proton™ System. With higher sensitivity and a broader dynamic range than arrays, the Ion AmpliSeq™ Transcriptome Solution enables researchers to profile the gene expression of over 20,000 RefSeq targets and requires as little as 10 ng of FFPE RNA.. The Ion AmpliSeq™ Transcriptome technology is a very useful tool for any group analyzing low input or FFPE samples using RNA-Seq. Our highly degraded, low yield, or microdissected samples that could not be successfully processed in the past now have a dependable and efficient conduit for library preparation.. Brad Hancock, Genomics Director ...
Laure Berti-Equille, Fouzia Moussouni, Anne Arcade. Integration of Biological Data on Transcriptome. Ingéniérie des Systèmes dInformation, Lavoisier, 2001, Numéro Spécial Interopérabilité et Intégration des Systèmes dInformation, 6 (3/2001), pp.61-86. ⟨hal-01856201⟩ ...
Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the
The Cancer Research Theme has developed an integrated, thematic programme which involves research across a number of areas including basic science, translation medicine, health economics and planning, and global health. Trinity researchers working in partnership with clinicians in the teaching hospitals St. Jamess, Tallaght (AMNCH), The National Paediatric Hospital and The Coombe Women and Infants University Hospital are making advances in both basic and translational research, improving the treatment, and management of cancer in a way that allows people to live good quality lives.. The Centre for Cancer Research in Trinity aims to educate and to expand knowledge and understanding for best practice with regards to cancer research, as well as develop new treatments and strategies through a combination of biomedical and biomolecular research. The main cancer research niche areas include: lung, ovary, cervix , oesophagus, breast, prostate, colon, salivary, thyroid/head and neck, multiple myeloma, ...
The transcriptome is the entire assembly of RNA transcripts in a given cell type, including protein coding and noncoding transcripts. Transcriptome sequencing (RNA-Seq) is a recently developed...
Hi Michael-. Thank you for your question. If this is your first time trying a cutting agent Id suggest you take a look at True Shred and see if that might be better for you. Anafuse helps to build more muscle and wont reduce as much fat, its a solid way to build a foundation of muscle prior to sculpting your physique or if you are just plain bulking. Anabolic Trinity is a three compound stack, someone who has done multiple cutting cycles would benefit more from Anabolic Trinity. True Shred is also a stack but is not just about building muscle. It has 7-keto and an estrogen blocker which work to help you build well defined hard lean muscle. It also contains a natural anabolic, Laxogenin, which helps you to maintain or grow muscle while you cut. The other thing nice about True Shred is that it doesnt require on cycle or post cycle therapy, thus its total cost is significantly less than that of Anabolic Trinity. In the end customers report very good results with both.. Thank you for your ...
D69F08P1:337:C4GGBACXX:1:1101:1123:2158_2:N:0:. I run Trinity with the code: ./Trinity --seqType fa --JM 180G --single 8_Trimmed.fa --run_as_paired --normalize_reads --SS_lib_type FR --min_contig_length 400 --CPU 6 --full_cleanup. output of trinity with error:. Paired mode requires bowtie. Found bowtie at: /usr/bin/bowtie. and bowtie-build at /usr/bin/bowtie-build. -since butterfly will eventually be run, lets test for proper execution of java. Found samtools at: /usr/bin/samtools. #######################################. Running Java Tests. Wednesday, June 24, 2015: 13:28:35 CMD: java -Xmx64m -jar /home/jafarinezhad/software/trinityrnaseq_r20140717/util/support_scripts/ExitTester.jar 0. CMD finished (1 seconds). Wednesday, June 24, 2015: 13:28:36 CMD: java -Xmx64m -jar /home/jafarinezhad/software/trinityrnaseq_r20140717/util/support_scripts/ExitTester.jar 1. -we properly captured the java failure status, as needed. Looking good.. Java tests ...
in Trinity County a few hundred to more than 9,000 feet. Through these hills and mountains flow numerous streams, nearly all of which are a part of the watershed of the Trinity River, which rises in the northern and eastern part of the county, and leaving the countys confines, empties into the Klamath River. Mining has been the principal industry of the county for more than fifty years. Other industries are farming, grazing and lumbering. Hydraulic, placer, drift, dredge and quartz mining are all followed with profitable results and there are still hundreds of acres of auriferous gravel awaiting exploration and many quartz veins that are untouched. Hydraulic mining is vigorously prosecuted in various parts of the county under conditions which enable that branch of mining to be conducted more advantageously than in any other part of the State. The placer grounds are so situated that the debris from their workings passes into the Trinity and finally into the Klamath River, which are unnavigable ...
Disclaimer. Trinity Delta Research Limited (TDRL; firm reference number: 725161), which trades as Trinity Delta, is an appointed representative of Equity Development Limited (ED). The contents of this report, which has been prepared by and is the sole responsibility of TDRL, have been reviewed, but not independently verified, by ED which is authorised and regulated by the FCA, and whose reference number is 185325.. ED is acting for TDRL and not for any other person and will not be responsible for providing the protections provided to clients of TDRL nor for advising any other person in connection with the contents of this report and, except to the extent required by applicable law, including the rules of the FCA, owes no duty of care to any other such person. No reliance may be placed on ED for advice or recommendations with respect to the contents of this report and, to the extent it may do so under applicable law, ED makes no representation or warranty to the persons reading this report ...
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Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We pr …
TUCSON, Ariz. , Feb. 05, 2020 (GLOBE NEWSWIRE) - HTG Molecular Diagnostics , Inc. (Nasdaq: HTGM) (HTG), a life science company whose mission is to advance precision medicine, today highlighted the reproducibility of the HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA), as reported in a. full press release. ...
The TransPlex Whole Transcriptome Amplification (WTA) Kits provide a simple, fast and accurate method of amplifying total RNA from a variety of sources that includes animals, plants and microorganisms.
TY - JOUR. T1 - Analyses of Avascular Mutants Reveal Unique Transcriptomic Signature of Non-conventional Endothelial Cells. AU - Pak, Boryeong. AU - Schmitt, Christopher E.. AU - Choi, Woosoung. AU - Kim, Jun Dae. AU - Han, Orjin. AU - Alsiö, Jessica. AU - Jung, Da Woon. AU - Williams, Darren R.. AU - Coppieters, Wouter. AU - Stainier, Didier Y.R.. AU - Jin, Suk Won. PY - 2020/11/23. Y1 - 2020/11/23. N2 - Endothelial cells appear to emerge from diverse progenitors. However, to which extent their developmental origin contributes to define their cellular and molecular characteristics remains largely unknown. Here, we report that a subset of endothelial cells that emerge from the tailbud possess unique molecular characteristics that set them apart from stereotypical lateral plate mesoderm (LPM)-derived endothelial cells. Lineage tracing shows that these tailbud-derived endothelial cells arise at mid-somitogenesis stages, and surprisingly do not require Npas4l or Etsrp function, indicating that ...
Table_4_Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo.xlsx
Defining the molecular transcriptomic profile for predicting the clinical outcome of anthracycline resistant breast cancers. Defining metastases in relation with the primary tumor. BREAST-OMICS
I am wondering how the removal of adaptor sequences will impact the transcriptome assembly. For example, in 10% of my reads contain adaptors which are not removed. If I try to assemble the transcriptome, will some of my unigene dataset contain adaptors? Besides, will the result be different if I use a genome-guided or de novo asssembly method?. ...
Analysis of transcriptome changes has become an established method to characterize the reaction of cells to toxicants. Such experiments are mostly performed at compound concentrations close to the cytotoxicity threshold. At present, little information is available on concentration-dependent features …
Make a new folder and move one transcriptome file under that folder. For example my folder was called PE111_Cabr_VNO_trinity_output and my transcriptome file was PE111_Cabr_VNO_trinity_output.Trinity.fasta ...
Comparison of Muscle Transcriptome between Pigs with Divergent Meat Quality Phenotypes Identifies Genes Related to Muscle Metabolism and Structure. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
A transcriptome sequencing study from researchers at the University of Texas has identified new gene co-expression networks associated with alcoholism.
Usability of reference-free transcriptome assemblies for detection of differential expression: A case study on Aethionema arabicum dimorphic ...
AMDs Trinity APUs have only been in the wild for a few days, but some have already taken on the challenge of pushing the new desktop silicon to its limits. By giving the A10-5800K model 1.956 volts, disabling two of its cores and cooling it with liquid nitrogen, overclockers were able to push the chip to 7.3GHz. Air-cooling and 1.616 volts squeezed out 5.1GHz without sacrificing any cores. If youre a mere mortal whos fresh out of liquid nitrogen (or never had any to begin with), you should be able to comfortably bump CPU performance by roughly 10 percent and GPU speeds by 15 to 17 percent. For the full specs on this particular overclock, hit the source links below.. Filed under: Desktops. AMD Trinity APU overclocked at 7.3 GHz, kept cool with liquid nitrogen originally appeared on Engadget on Sat, 06 Oct 2012 09:04:00 EDT. Please see our terms for use of feeds. ...
Self-distribution initiative binds supply chain with Trinity Healths larger goal - improving the delivery of cost-effective, people-centered care.. Trinity Health has a certain way of doing things. Its something Lou Fierens, senior vice president, supply chain and fixed asset management, talks about a lot. Its a way of delivering care, and it permeates the IDN, including supply chain.. Having a way of doing things connotes forethought, collaboration and discipline - all good things for an IDN the size of Trinity (with hospitals in 21 states), which is trying to create economies of scale and a uniform, high-quality care-delivery process. And all things for which Fierens has been laying the groundwork since coming to Trinity in 2001.. In March, Trinitys supply chain team announced the next step on its way, when it announced plans to build - with XPO Logistics - the first of four Trinity Health supply distribution centers.. XPO Logistics will manage and operate the $26 million facility in Fort ...
Trinity county, California Plants Allergy Info for Research - Complete Online Significant Allergens and Plants Reference for Trinity county in Winter
De novo Transcriptome Sequencing of Cold-treated Kentucky Bluegrass (Poa pratensis) and Analysis of the Genes Involved in Cold Tolerance Abstract.
Plukenetia volubilis is a promising oilseed crop due to its seeds being rich in unsaturated fatty acids, especially alpha-linolenic acid. P. volubilis is monoecious, with separate male and female flowers on the same inflorescence. We previously reported that male flowers were converted to female flowers by exogenous cytokinin (6-benzyladenine, 6-BA) treatment in P. volubilis. To identify candidate genes associated with floral sex differentiation of P. volubilis, we performed de novo transcriptome assembly and comparative analysis on control male inflorescence buds (MIB) and female inflorescence buds (FIB) induced by 6-BA using Illumina sequencing technology. A total of 57,664 unigenes with an average length of 979 bp were assembled from 104.1 million clean reads, and 45,235 (78.45%) unigenes were successfully annotated in the public databases. Notably, Gene Ontology analyses revealed that 4193 and 3880 unigenes were enriched in the categories of reproduction and reproductive processes, ...
The availability and throughput of next generation sequencing technologies has enabled the rapid and efficient sequencing of transcriptomes for model and non-model species. The majority of de novo transcriptome assemblies in non-model organisms have in the past been produced using the long reads (300-600 bp) generated using Roche 454 [24]. With the recent developments in sequencing technology, short read sequencers (90-400 bp), such as Illumina and Ion Torrent, are starting to be more commonly used for the generation of large next generation sequencing data sets, as the costs are much lower for the same output [25]. Consequently, the use of short read sequencers to generate de novo transcriptome assemblies for non-model organisms may lead to a more complete gene set for these species at a lower cost. The reliability of de novo transcriptome assemblies generated from short read sequencers, however, needs to be validated to ensure that assemblies are accurate and wont compromise the downstream ...
Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. ...
TY - JOUR. T1 - Altered transcriptome signature of phenotypically normal skin fibroblasts heterozygous for CDKN2A in familial melanoma. T2 - Relevance to early intervention. AU - Fan, Meiyun. AU - Pfeffer, Susan R.. AU - Lynch, Henry T.. AU - Cassidy, Pamela. AU - Leachman, Sancy. AU - Pfeffer, Lawrence M.. AU - Kopelovich, Levy. PY - 2013. Y1 - 2013. N2 - Familial melanoma (FM) is a dominantly heritable cancer that is associated with mutations in the tumor suppressor CDKN2A/p16. In FM, a single inherited hit occurs in every somatic cell, enabling interrogation of cultured normal skin fibroblasts (SFs) from FM gene carriers as surrogates for the cell of tumor origin, namely the melanocyte.We compared the gene expression profile of SFs from FM individuals with two distinct CDKN2A/p16 mutations (V126D-p16 and R87P-p16) with the gene expression profile of SFs from age-matched individuals without p16 mutations and with no family history of melanoma. We show an altered transcriptome signature in ...
Since about 1000 A.D. the lower Trinity River has been inhabited by the Natinixwe, now known as the Hupa people.[37]:31 Natinixwe is an endonym meaning people of the place where the trails return. Their name for the Trinity River was hun simply meaning river.[38] The name Hupa or Hoopa appears to originate from the Yurok word for the Trinity River country, hopah, which was first recorded by ethnologist George Gibbs in 1852.[39]:3-5. The Hupa lived in the fertile Hoopa Valley along the Trinity River and the Hyampom Valley on the South Fork - some of the few flat lands in a region otherwise dominated by rugged mountains. A Hupa village called Weitspus stood at the site of present-day Weitchpec at the confluence of the Trinity and Klamath Rivers.[40] The Hupa traded with the coastal Yurok and Karok by using canoes to navigate the Trinity and Klamath Rivers. The trade arrangements with neighboring tribes were complex and involved the use of dentalium shells as currency.[41]. The Chimariko ...
Plant natural product research can be facilitated through genome and transcriptome sequencing approaches that generate informative sequence and expression datasets that enable characterization of biochemical pathways of interest. As the overwhelming majority of plant-derived natural products are derived from Modern Methods in Plant Natural Products
In the present study, we established a novel TNBC classification system, the FUSCC classification, by integrating the expression profiles of both mRNAs and lncRNAs. TNBC samples can be clearly classified into four subtypes according to our system: IM, LAR, MES, and BLIS. Each subtype has its own unique transcriptome profile. Furthermore, we filtrated out several subtype-specific lncRNAs and predicted possible functions of these lncRNAs in TNBC biological processes by analyzing the co-expression network between lncRNAs and mRNAs. To the best of our knowledge, the present study is the first to develop a novel TNBC classification system based on the transcriptome profiles of both mRNAs and lncRNAs in a large TNBC cohort.. Several novel findings were revealed in our in-depth transcriptome analysis. First, considering the expanding roles of lncRNAs in tumorigenesis and disease development, we integrated the expression profiles of both mRNAs and lncRNAs in an attempt to comprehensively understand the ...
Scientists from the Marine Biological Laboratory and Brown University developed a new pipeline for de novo transcriptome assembly that can be used with organisms lacking a well-annotated reference genome. The paper describes library preparation and computational analysis processes. Pippin Prep was used for size selection in a standard Illumina workflow and also in conjunction with an Epicentre ScriptSeq™ kit.. Citation: ...
Reid, Robert W.,Luo, Yan,Yan, Sue,et al. Transcriptome Dataset Of Halophyte Beach Morning Glory, A Close Wild Relative Of Sweet Potato[J]. Frontiers In Plant Science,2016,7(X ...
TY - JOUR. T1 - Analysis of global transcriptome change in mouse embryonic fibroblasts after dsDNA and dsRNA viral mimic stimulation. AU - Xie, Xin. AU - Liu, Pu Ste. AU - Percipalle, Piergiorgio. PY - 2019. Y1 - 2019. N2 - The activation of innate immunity by viral nucleic acids present in the cytoplasm plays an essential role in controlling viral infection in both immune and non-immune cells. The dsDNA and dsRNA viral mimics can stimulate the cytosolic nucleic acids sensors and activate the antiviral innate immunity. In this study, taking advantage of dsDNA and dsRNA viral mimics, we investigated the global transcriptome changes after the antiviral immunity activation in mouse embryonic fibroblasts. Results from our data identified a positive feedback up-regulation of sensors (e.g., Tlr2, Tlr3, Ddx58, cGAS), transducers (e.g., Traf2, Tbk1) and transcription factors (e.g., Irf7, Jun, Stat1, Stat2) in multiple pathways involved in detecting viral or microbial infections upon viral mimic ...
Background: Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian 6 Landrace backcross with extreme phenotypes according to FA profile. Results: We sequenced the muscle transcriptome acquiring 787.5 M of 75 bp paired-end reads. About 85.1% of reads were mapped to the reference genome. Of the total reads, 79.1% were located in exons, 6.0% in introns and 14.9% in intergenic regions, indicating expressed regions not annotated in the reference genome. We identified a 34.5% of the intergenic regions as interspersed repetitive regions. We predicted a total of 2,372 putative proteins. Pathway analysis with 131 differentially-expressed genes revealed that the most statistically-significant metabolic pathways were related with
We identified 7584 pairs of one-to-one orthologous transcripts between the two transcriptomes (see Table S2) and 7851 and 21,980 nonone-to-one orthologous transcripts for PA-Microphallus and PE-Microphallus, respectively. The two one-to-one ortholog transcriptomes contain higher mean transcript lengths (18.6% longer for PA-Microphallus; 38.7% longer for PE-Microphallus) and larger N50 values (11.7% greater N50 for PA-Microphallus; 33.9% greater N50 for PE-Microphallus) than their corresponding reference transcriptomes (Table 1). The longer transcripts and higher N50 values in the one-to-one ortholog sets relative to the reference transcriptomes indicate that the one-to-one orthologs represent a set of approximately full-length high quality genes that occur once and only once in both transcriptome assemblies. More than half (PA-Microphallus: 51.7%; PE-Microphallus: 51.2%) of the BUSCO genes are retained in this reduced gene set, further indicating that our filtering steps likely removed poor ...
Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. ...
Blood is an ideal tissue for the identification of novel genomic biomarkers for toxicity or efficacy. However, using blood for transcriptomic profiling presents significant technical challenges due to the transcriptomic changes induced by ex vivo handling and the interference of highly abundant globin mRNA. Most whole blood RNA stabilization and isolation methods also require significant volumes of blood, limiting their effective use in small animal species, such as rodents. To overcome these challenges, a QIAzol-based RNA stabilization and isolation method (QSI) was developed to isolate sufficient amounts of high quality total RNA from 25 to 500 μL of rat whole blood. The method was compared to the standard PAXgene Blood RNA System using blood collected from rats exposed to saline or lipopolysaccharide (LPS). The QSI method yielded an average of 54 ng total RNA per μL of rat whole blood with an average RNA Integrity Number (RIN) of 9, a performance comparable with the standard PAXgene method. Total
Search and download thousands of Swedish university dissertations (essays). Full text. Free. Dissertation: Transcriptome-wide analysis in cells and tissues.
TY - JOUR. T1 - Genome2D. T2 - a visualization tool for the rapid analysis of bacterial transcriptome data.. AU - Baerends, Richard J.S.. AU - Smits, Wiep Klaas. AU - de Jong, Anne. AU - Hamoen, Leendert W.. AU - Kok, Jan. AU - Kuipers, Oscar P.. PY - 2004. Y1 - 2004. N2 - Genome2D is a Windows-based software tool for visualization of bacterial transcriptome and customized datasets on linear chromosome maps constructed from annotated genome sequences. Genome2D facilitates the analysis of transcriptome data by using different color ranges to depict differences in gene-expression levels on a genome map. Such output format enables visual inspection of the transcriptome data, and will quickly reveal transcriptional units, without prior knowledge of expression level cutoff values. The compiled version of Genome2D is freely available for academic or non-profit use from http://molgen.biol.rug.nl/molgen/research/molgensoftware.php.. AB - Genome2D is a Windows-based software tool for visualization of ...
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Purpose: By integrating expression profiles of mRNAs and long noncoding RNAs (lncRNA), we tried to develop and validate novel multigene signatures to facilitate individualized treatment of triple-negative breast cancer (TNBC) patients.. Experimental Design: We analyzed 165 TNBC samples and 33 paired normal breast tissues using transcriptome microarrays. Tumor-specific mRNAs and lncRNAs were identified and correlated with patients recurrence-free survival (RFS). Using Cox regression model, we built two multigene signatures incorporating mRNAs and lncRNAs. The prognostic and predictive accuracy of the signatures were tested in a training set of 165 TNBC patients and validated in other 101 TNBC patients.. Results: We successfully developed an mRNA and an integrated mRNA-lncRNA signature based on eight mRNAs and two lncRNAs. In the training set, patients in the high-risk group were more likely to suffer from recurrent disease than patients in the low-risk group in both signatures [HR, 10.00; 95% ...
RNA-Seq based transcriptome assembly has been widely used to identify novel lncRNAs. However, the best-performing transcript reconstruction methods merely identified 21% of full-length protein-coding transcripts from H. sapiens. Those partial-length protein-coding transcripts are more likely to be classified as lncRNAs due to their incomplete CDS, leading to higher false positive rate for lncRNA identification. Furthermore, potential sequencing or assembly error that gain or abolish stop codons also complicates ORF-based prediction of lncRNAs. Therefore, it remains a challenge to identify lncRNAs from the assembled transcripts, particularly the partial-length ones.. Here, researchers from the University of Southern California present a novel alignment-free tool, lncScore, which uses a logistic regression model with 11 carefully selected features. Compared to other state-of-the-art alignment-free tools (e.g. CPAT, CNCI, and PLEK), lncScore outperforms them on accurately distinguishing lncRNAs ...
RNA-sequencing is a new method of transcriptome characterization of organisms. Based on identity and relatedness, there are large genetic variations among different cattle breeds. The goal of the current study was to sequence the transcriptome of Guilan native cow and compare with available reference genome using RNA-sequencing method. Blood samples were collected from 14 Guilan native cows and then were pooled with same ratios of 3 micrograms per sample. Sequencing of the pooled sample was carried out using Illumina Hiseq 2000 from both end and 100 base pair of reading length. Tophat2 software was used to align the reads with reference genome and identify splice junctions and insertions and deletions. Cufflinks software was used to assemble transcripts and calculate their abundances. Total numbers of sequenced RNA fragments were 28434708 and the overall reading map was 87.4 percent. Total numbers of expressed genes were 24616 genes, which 19994 genes from these were protein coding genes and 3825 genes
Background: A molecular process based genotype-to-phenotype map will ultimately enable us to predict how genetic variation among individuals results in phenotypic alterations. Building such a map is, however, far from straightforward. It requires understanding how molecular variation reshapes developmental and metabolic networks, and how the functional state of these networks modifies phenotypes in genotype specific way. We focus on the latter problem by describing genetic variation in transcript levels of genes in the InR/TOR pathway among 72 Drosophila melanogaster genotypes. Results: We observe tight co-variance in transcript levels of genes not known to influence each other through direct transcriptional control. We summarize transcriptome variation with factor analyses, and observe strong co-variance of gene expression within the dFOXO-branch and within the TOR-branch of the pathway. Finally, we investigate whether major axes of transcriptome variation shape phenotypes expected to be influenced
Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non-model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to annotate each predicted contig as either a full-length cDNA, fragment, chimera, allele, paralogue, genomic ...
TY - JOUR. T1 - Epigenomic and transcriptomic approaches in the post-genomic era. T2 - path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heartd. AU - Perrino, Cinzia. AU - Barabasi, Albert-Laszlo. AU - Condorelli, Gianluigi. AU - Davidson, Sean Michael. AU - De Windt, Leon. AU - Dimmeler, Stefanie. AU - Engel, Felix Benedikt. AU - Hausenloy, Derek John. AU - Hill, Joseph Addison. AU - Van Laake, Linda Wilhelmina. AU - Lecour, Sandrine. AU - Leor, Jonathan. AU - Madonna, Rosalinda. AU - Mayr, Manuel. AU - Prunier, Fabrice. AU - Sluijter, Joost Petrus Geradus. AU - Schulz, Rainer. AU - Thum, Thomas. AU - Ytrehus, Kirsti. AU - Ferdinandy, Peter. PY - 2017/6/1. Y1 - 2017/6/1. KW - Big Data. KW - Omics. KW - Multiomics. KW - Tailored medicine. KW - Bioinformatics. KW - Network analysis. KW - CARDIAC GENE-EXPRESSION. KW - DNA METHYLATION. KW - NONCODING RNAS. KW - REPERFUSION ...
RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such as Illumina Next-Seq have yielded easy-to-operate machines, with high throughput, at a lower price per base. However, processing this data requires bioinformatics expertise to tailor and execute specific solutions for each type of library preparation. In order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline that executes the full process, starting from cDNA sequences derived by RNA-Seq [Nat Rev Genet 10:57-63, 2009] and bulk MARS-Seq [Science 343:776-779, 2014] and ending with sets of differentially expressed genes. Output files are placed in structured folders, and results summaries are provided in rich and comprehensive reports, containing dozens of plots, tables and links. Our User-friendly Transcriptome Analysis Pipeline (UTAP) is an
The transcriptome can be described in plants, including in fruit tree species, as the complete list of all types of RNA molecules expressed in a cell, tissue or whole organism. The transcriptome comprises the protein-coding RNA (messenger RNA, mRNA) and the noncoding RNA, including the noncoding, non-regulatory RNA [ribosomal RNA (rRNA) and transfer RNA (tRNA)] and the noncoding regulatory RNA [small interfering RNA (siRNA); micro RNA (miRNA); small nucleolar RNA (snoRNA); piwi-interacting RNA (piRNA); long noncoding RNA (lncRNA), etc.]. First works on transcriptome analysis in fruit tree species started at the mRNA level in the early 2000s with cDNA-AFLP (cDNA Amplified Fragment Length Polymorphism) analysis, the development of ESTs (expressed sequence tags) and the analysis of several candidate genes. More recently, new strategies of massive analysis (high-throughput) of transcriptomes have been applied, producing larger amounts of data in terms of expression of a large number of genes in a single
The transition of the human uterus from a quiescent to a contractile state takes place over a number of weeks. On such biological time scales, cellular phenotype is modified by changes in the transcriptome, which in turn is under the control of the underlying endocrine, paracrine, and biophysical processes resulting from the ongoing pregnancy. In this study, we characterize the transition of the human myometrial transcriptome at term from not in labour (NIL) to in labour (LAB) using high throughput RNA sequencing (RNA-seq). RNA was isolated from the myometrium of uterine biopsies from patients at term who were not in labour (n = 5) and at term in spontaneous labour (n = 5) without augmentation. A total of 143.6 million separate reads were sequenced, achieving, on average, ∼13 times coverage of the expressed human transcriptome per sample. Principal component analysis indicated that the NIL and LAB transcriptomes could be distinguished as two distinct clusters. A comparison of the NIL and LAB ...
Contact. Please see Turkey - contacts and further information for details in your area.. How to become a Registered Centre Please see Become a Registered Exam Centre with Trinity.. Candidate enrolment. For more information or to enrol for exams, please contact the Trinity local representative in your area.. Exam dates. Further details will be available shortly.. If a candidate is absent due to illness or family emergency, the candidate can be offered a re-entry voucher for 50% of the fee paid which is valid for one year. Appropriate documentation must be submitted to the Trinity office within a week of the missed exam.. ...
Join the likes of Oscar Wilde, Samuel Beckett, Mary Robinson, and other distinguished alumni who studied at Irelands oldest and highest-ranked university and CIEEs partner school - Trinity College Dublin. Choose from a wide-range of courses across three colleges: Arts, Humanities, and Social Sciences; Engineering, Mathematics, and Science; and Health Sciences. Students can opt to take a full course load at Trinity (five courses per semester) or combine Trinity courses with CIEE electives, taught by adjunct lecturers at CIEE Dublin, located on Dublin City Universitys All Hallows campus. All courses are complemented with CIEE co-curricular activities and excursions beyond the city to make your understanding of Ireland complete - and unforgettable.. ...
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Stranded whole transcriptome RNA‐Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to, miRNA (microRNA), piRNA (Piwi‐interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non‐coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA), and mRNA (messenger RNA)
The biological function of a gene often depends on spatial context, and an atlas of transcriptional regulation could be instrumental in defining functional elements across the genome. Despite recent advances in single-cell RNA sequencing and in situ RNA imaging, fundamental barriers limit the speed, genome-wide coverage, and resolution of de novo transcriptome assembly in space. Here, I discuss potential next-generation approaches for the de novo assembly of the transcriptome in space, and propose more efficient methods of detecting long-range spatial variations in gene expression. Finally, I discuss future in situ sequencing chemistries for visualizing biological pathways and processes in tissues so that genomics technologies might be more easily applied to conditions of human health and disease.. ...
Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa Yaan and H. altissima 1110. Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for Yaan and 1110, respectively. In addition, a total of 86,731 Yawn and 48,645 1110 unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were ...
BACKGROUND: The precise function of various resting and activated leukocyte subsets remains unclear. For instance, mast cells, basophils, and eosinophils play important roles in allergic inflammation but also participate in other immunologic responses. One strategy to understand leukocyte subset function is to define the expression and function of subset-restricted molecules. OBJECTIVE: To use a microarray dataset and bioinformatics strategies to identify novel leukocyte markers as well as genes associated with allergic or innate responses. METHODS: By using Affymetrix microarrays, we generated an immune transcriptome dataset composed of gene profiles from all of the major leukocyte subsets, including rare enigmatic subsets such as mast cells, basophils, and plasma cells. We also assessed whether analysis of genes expressed commonly by certain groups of leukocytes, such as allergic leukocytes, might identify genes associated with particular responses. RESULTS: Transcripts highly restricted to a single
Elymus L. is the largest genus in the tribe Triticeae Dumort., encompassing approximately 150 polyploid perennial species widely distributed in the temperate regions of the world. It is considered to be an important gene pool for improving cereal crops. However, a shortage of molecular marker limits the efficiency and accuracy of genetic breeding for Elymus species. High-throughput transcriptome sequencing data is essential for gene discovery and molecular marker development. We obtained the transcriptome dataset of E. sibiricus, the type species of the genus Elymus, and identified a total of 8871 putative EST-SSRs from 6685 unigenes. Trinucleotides were the dominant repeat motif (4760, 53.66%), followed by dinucleotides (1993, 22.47%) and mononucleotides (1876, 21.15%). The most dominant trinucleotide repeat motif was CCG/CGG (1119, 23.5%). Sequencing of PCR products showed that the sequenced alleles from different Elymus species were homologous to the original SSR locus from which the primer was
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Assessing the impact of global warming on the food web of the North Atlantic will require difficult-to-obtain physiological data on a key copepod crustacean, Calanus finmarchicus. The de novo transcriptome presented here represents a new resource for acquiring such data. It was produced from multiplexed gene libraries using RNA collected from six developmental stages: embryo, early nauplius (NI-II), late nauplius (NV-VI), early copepodite (CI-II), late copepodite (CV) and adult (CVI) female. Over 400,000,000 paired-end reads (100 base-pairs long) were sequenced on an Illumina instrument, and assembled into 206,041 contigs using Trinity software. Coverage was estimated to be at least 65%. A reference transcriptome comprising 96,090 unique components (
Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of ,2,400 previously unannotated transcripts ...
Stephanoeca diplocostata transcriptome[edit]. The first transcriptome of a loricate choanoflagellate[30] led to the discovery ... Monosiga ovata transcriptome[edit]. An EST dataset from Monosiga ovata was published in 2006.[33] The major finding of this ... Genomes and transcriptomes[edit]. Two choanoflagellate species have had their genomes fully sequenced, with another two species ... having had transcriptome data published. Monosiga brevicollis genome[edit]. The genome of Monosiga brevicollis, with 41.6 ...
Single-cell transcriptome sequencing (scRNA-seq)[edit]. Standard methods such as microarrays and bulk RNA-seq analysis analyze ... May 2009). "mRNA-Seq whole-transcriptome analysis of a single cell". Nature Methods. 6 (5): 377-82. doi:10.1038/NMETH.1315. ... September 2009). "Digital transcriptome profiling using selective hexamer priming for cDNA synthesis". Nature Methods. 6 (9): ... The first single-cell transcriptome analysis in a prokaryotic species was accomplished using the terminator exonuclease enzyme ...
Other than transcriptome shotgun sequencing, this technique has been called RNA-seq and whole transcriptome shotgun sequencing ... One Thousand Plant Transcriptomes Initiative (October 2019). "One thousand plant transcriptomes and the phylogenomics of green ... Since only the transcriptome was sequenced, the project did not reveal information about gene regulatory sequence, non-coding ... A new a de novo transcriptome assembler designed specifically for RNA-Seq was produced for this project, SOAPdenovo-Trans being ...
The control Transcriptomes users are able to use them as an avatar, such as Camael. Usually, Quanxs are born naturally, but ... They're Transcriptome. He appeared as a character of Denma with NAVER WEBTOON. He appeared as a hero in Densinma with NAVER ... The object Quanx Transcriptome is one of the most fiercely competed secret project done by the universe eight munitions ... She's Yahwah's Transcriptome. Arcel (Korean: 아셀; RR: Asel): He's first appeared in Chapter 1 Ep. 4 - Eve Rachel (2) - #14. He ...
TranscriptomeEdit. In 2010, Sharma et al. presented a comprehensive analysis of transcription at single-nucleotide resolution ... "The primary transcriptome of the major human pathogen Helicobacter pylori". Nature. 464 (7286): 250-255. Bibcode:2010Natur.464 ...
"Illumina bodyMap2 transcriptome". NCBI (National Center for Biotechnology Information) BioProject. Szabo L, Morey R, Palpant NJ ... April 2004). "A gene atlas of the mouse and human protein-encoding transcriptomes". Proceedings of the National Academy of ...
Hrdlickova R, Toloue M, Tian B (2017 January). "RNA-Seq methods for transcriptome analysis". Wiley Online Library. 8(1). ... Cieślik M, Chinnaiyan AM (2018 February). "Cancer transcriptome profiling at the juncture of clinical translation". Nature ... Martin JA, Wang Z (2011 September). "Next-generation transcriptome assembly". Nature Reviews Genetics. 12(10):671-82. 10.1038/ ... "Single-cell sequencing of the small-RNA transcriptome". Nature Biotechnology. 34(12):1264-1266. 10.1038/nbt.3701. PMID 27798564 ...
Deciphering the Cancer Transcriptome. 2016 Vega F, Medeiros LJ (September 2003). "Chromosomal translocations involved in non- ... March 2009). "Transcriptome sequencing to detect gene fusions in cancer". Nature. 458 (7234): 97-101. Bibcode:2009Natur.458... ... However, the precondition for large scale detection is a paired-end sequencing of the cell's transcriptome. The direction of ... Some researchers already developed a new tool called Transcriptome Viewer (TViewer) to directly visualize detected gene fusions ...
Goh SH, Josleyn M, Lee YT, Danner RL, Gherman RB, Cam MC, Miller JL (July 2007). "The human reticulocyte transcriptome". ...
GeneCalling, an mRNA profiling technology Missense mRNA mRNA display mRNA surveillance Transcriptome, the sum of all RNA in a ... "The human mitochondrial transcriptome". Cell. 146 (4): 645-658. doi:10.1016/j.cell.2011.06.051. PMC 3160626. PMID 21854988. ...
Multicellgenome, Lab; Guifré, Torruella (2017-09-26). "Transcriptome - Parvularia atlantis (Nuclearia sp. ATCC 50694)". ...
A transcriptome sequence is determined. Paramecium bursaria with green zoochlorellae living inside endosymbiotically A ...
Single-cell transcriptomes are now well described and have even been extended to in situ RNA-Seq where transcriptomes of ... Transcriptome databases have grown and increased in utility as more transcriptomes are collected and shared by researchers. It ... Aging has been shown to be a strong driver of transcriptome changes. Aging clocks based on transcriptomes have suffered from ... RNA-Seq leverages deep sampling of the transcriptome with many short fragments from a transcriptome to allow computational ...
Spellman and Rubin (2002) made a transcriptome map of Drosophila. Of all assayed genes 20% was clustered. Clusters consisted of ... Yamashita T, Honda M, Takatori H, Nishino R, Hoshino N, Kaneko S (November 2004). "Genome-wide transcriptome mapping analysis ... 2001) made a human transcriptome map of 12 different tissues (cancer cells) and concluded that genes are not randomly ... September 2003). "The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern ...
Kocabas, A. M., Crosby, J., Ross, P. J., Otu, H. H., Beyhan, Z., Can, H., ... & Fernandez, E. (2006). The transcriptome of ...
These studies led Velculescu to coin the term transcriptome in a 1997 paper to describe the comprehensive gene expression ... "Characterization of the yeast transcriptome". Cell. 88 (2): 243-51. doi:10.1016/s0092-8674(00)81845-0. PMID 9008165. S2CID ...
Mutations in the insect transcriptome. J Clin Exp Pathol. 2016; 6: 3. 13. Picimbon JF. A new view of genetic mutations. ... Transcriptome exploration of the sex pheromone gland of Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae). Parasit ... Zhu J, Wang G, Pelosi P. Plant transcriptomes reveal hidden guests. Biochem Biophys Res Commun. 2016; 474: 497-502. 27. Perkin ...
Antennal transcriptome of Manduca sexta. Proceedings of the National Academy of Sciences of the United States of America, 108, ...
Human Genome Project In silico Transcriptome Genesis Partners List of Israeli companies quoted on the Nasdaq Compugen 2016 ... CS1 maint: discouraged parameter (link) Xie, Hanqing; Gill-More, Raveh (2004). "Transcriptome Analysis Through Expressed ...
"The transcriptome of human oocytes". Proceedings of the National Academy of Sciences of the United States of America. 103 (38 ... "The transcriptome of human oocytes". Proceedings of the National Academy of Sciences of the United States of America. 103 (38 ...
Casella G, Munk R, Kim KM, Piao Y, De S, Abdelmohsen K, Gorospe M (August 2019). "Transcriptome signature of cellular ...
"Transcriptome analysis of human gastric cancer". Mammalian Genome. 16 (12): 942-54. doi:10.1007/s00335-005-0075-2. PMID ...
"Transcriptome analysis of human gastric cancer". Mamm. Genome. 16 (12): 942-54. doi:10.1007/s00335-005-0075-2. PMID 16341674. ...
"The antisense transcriptomes of human cells". Science. 322 (5909): 1855-7. Bibcode:2008Sci...322.1855H. doi:10.1126/science. ... "Antisense transcription in the mammalian transcriptome". Science. 309 (5740): 1564-6. Bibcode:2005Sci...309.1564R. doi:10.1126/ ...
PMID 15487671.[dead link] Wirta W (2006). Mining the transcriptome - methods and applications. Stockholm: School of ... virus DNA History of RNA Biology List of RNA Biologists RNA Society Macromolecule RNA-based evolution RNA origami Transcriptome ...
Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A (December 2007). "The expanding RNA polymerase III transcriptome". ...
Hrdlickova, Radmila; Toloue, Masoud; Tian, Bin (January 2017). "RNA-Seq methods for transcriptome analysis". Wiley ... "Sequencing of first-strand cDNA library reveals full-length transcriptomes". Nature Communications. 6 (1): 6002. Bibcode: ...
Clogmia albipunctata, moth midge (transcriptome 2013[124]). *Culex quinquefasciatus, mosquito (vector of West Nile virus, ... "Genome and transcriptome of the porcine whipworm Trichuris suis". Nature Genetics. 46 (7): 701-6. doi:10.1038/ng.3012. PMC ... "The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery". Genome Biology. 14 ... "The duck genome and transcriptome provide insight into an avian influenza virus reservoir species". Nature Genetics. 45 (7): ...
The existence of an RNAP III-dependent ncRNA transcriptome that regulates its RNAP II-dependent counterpart was supported by a ... The complexity of the transcriptome, and our evolving understanding of its structure may inform a reinterpretation of the ... Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A (December 2007). "The expanding RNA polymerase III transcriptome". ... September 2005). "Antisense transcription in the mammalian transcriptome". Science. 309 (5740): 1564-6. Bibcode:2005Sci... ...
"Antisense transcription in the mammalian transcriptome". Science. 309 (5740): 1564-6. doi:10.1126/science.1112009. PMID ... "The antisense transcriptomes of human cells". Science. 322 (5909): 1855-7. doi:10.1126/science.1163853. PMC 2824178. PMID ...
The transcriptome is the set of all RNA molecules in one cell or a population of cells. It is sometimes used to refer to all ... Transcriptomes may also be used to infer phylogenetic relationships among individuals. Relation to proteome[edit]. Further ... The transcriptome can be seen as a subset of the proteome, that is, the entire set of proteins expressed by a genome. ... The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the ...
transcriptome (plural transcriptomes). *(biochemistry, genetics) The complete set of RNA molecules (transcripts) produced in a ... Retrieved from "https://en.wiktionary.org/w/index.php?title=transcriptome&oldid=46803573" ...
Transcriptome What is a Transcriptome Sequence? An organisms genes are expressed, that is transcribed from the genomes DNA ... Once a transcriptome has been sequenced, we can use the information to identify which parts of the genome are used to code for ... The set of genes which are transcribed in any one condition is known as the transcriptome, and the process of determining the ... If several transcriptomes have been sequenced under different growth or environmental conditions, we can start to estimate ...
Analyzing the transcriptome shows the genes which are being actively transcribed and can therefore yield highly informative ... The transcriptome is the full set of messenger RNA (mRNA) a cell has transcribed. Analyzing the transcriptome shows the genes ... Applications of transcriptome analyses. Studying gene regulation. Tissue-specific transcriptome analysis via NGS technology has ... The transcriptome can give us information about what the cell is actively doing or will do in the future. It also specifies the ...
Microfluidic single-cell whole-transcriptome sequencing. Aaron M. Streets, Xiannian Zhang, Chen Cao, Yuhong Pang, Xinglong Wu, ... With 0.2 M reads per cell, we were able to reconstruct a majority of the bulk transcriptome with 10 single cells. We also ... Single-cell whole-transcriptome analysis is a powerful tool for quantifying gene expression heterogeneity in populations of ... Many techniques have, thus, been recently developed to perform transcriptome sequencing (RNA-Seq) on individual cells. To probe ...
Artemis-users] transcriptome plot with DNAPlotter Lena Koenig. * *Re: [Artemis-users] transcriptome plot with DNAPlotter Tim ... Re: [Artemis-users] transcriptome plot with DNAPlotter Tim Carver Tue, 08 Nov 2011 01:11:31 -0800 ... but I cannot figure out how to create a transcriptome plot. , What type of input file is needed in addition to an annotation ...
Transcriptome sequencing (RNA-Seq) is a recently developed... ... The transcriptome is the entire assembly of RNA transcripts in ... Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009;458(7234):97-101.PubMedPubMedCentralGoogle Scholar ... Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol. 2010;13(5):619-24.PubMedPubMedCentralGoogle Scholar ... Chromosomal instability and transcriptome dynamics in cancer. Cancer Metastasis Rev. 2013;32(3-4):391-402.PubMedGoogle Scholar ...
transcriptome synonyms, transcriptome pronunciation, transcriptome translation, English dictionary definition of transcriptome ... transcriptome. Also found in: Medical, Wikipedia.. Related to transcriptome: gene expression. transcriptome. (trænˈskrɪptəʊm) n ... In the present study, we re-assembled the transcriptome datasets of B.. Comparative transcriptome analysis of three Bactrocera ... Transcriptome - definition of transcriptome by The Free Dictionary https://www.thefreedictionary.com/transcriptome ...
Transcriptome analysis shows similarity of expression patterns for all plants exposed to nanoparticles and a low impact on gene ... De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of ... We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity ... In the grapevine transcriptome, during the initial stages of leaf development 1Avs2A showed single transcript was down- ...
... The tammar wallaby (Macropus eugenii) is a kangaroo species native to islands ... international Tammar Wallaby Genome Sequencing Consortium present the tammar wallaby genome and transcriptome sequences. These ...
Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular ... Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular ...
The data show a unique signature in the Pseudomonas aeruginosa transcriptome in response to perturbation of outer membrane ... From Intracellular Bacteria to Differentiated Bacteroids: Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using ...
A 6.9 million-feature oligonucleotide array of the human transcriptome [Glue Grant human transcriptome (GG-H array)] has been ... Human transcriptome array for high-throughput clinical studies. Weihong Xu, Junhee Seok, Michael N. Mindrinos, Anthony C. ... Human transcriptome array for high-throughput clinical studies. Weihong Xu, Junhee Seok, Michael N. Mindrinos, Anthony C. ... Human transcriptome array for high-throughput clinical studies. Weihong Xu, Junhee Seok, Michael N. Mindrinos, Anthony C. ...
Single-cell transcriptome analysis of endometrial tissue.. Krjutškov K1, Katayama S2, Saare M3, Vera-Rodriguez M4, Lubenets D5 ... Although single-cell transcriptome analyses from various biopsied tissues have been published recently, corresponding protocols ... How can we study the full transcriptome of endometrial stromal and epithelial cells at the single-cell level? ... the amount of transcriptome data per individual epithelial cell was low, complicating further analysis. This step most likely ...
The core meiotic transcriptome in budding yeasts.. Primig M1, Williams RM, Winzeler EA, Tevzadze GG, Conway AR, Hwang SY, Davis ...
Though the transcriptomes eventually reverted back to that of the median cells, while they differed they could drive the cells ... Despite clonality, the Sca-1 outliers had distinct transcriptomes. Although their unique gene expression profiles eventually ... but reflects metastable states of a slowly fluctuating transcriptome that is distinct in individual cells and may govern the ... but rather is a manifestation of metastable states of a slowly fluctuating transcriptome. These fluctuations may govern the ...
Transcriptome Analysis. Edited by: Miroslav Blumenberg. ISBN 978-1-78984-327-9, eISBN 978-1-78984-328-6, PDF ISBN 978-1-78985- ... 3. Transcriptome Atlas by Long-Read RNA Sequencing: Contribution to a Reference Transcriptome. By Dong Jin Lee and Chang Pyo ... Transcriptome analysis is the study of the transcriptome, of the complete set of RNA transcripts that are produced under ... Transcriptome analysis is the study of the transcriptome, of the complete set of RNA transcripts that are produced under ...
The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to ... We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment ... this work paves the way for further HERV transcriptome projects. ... HERV Transcriptome Views. We provided a microarray-based ... Transcriptome analysis Is the Subject Area "Transcriptome analysis" applicable to this article? Yes. No. ...
Transcriptome is the RNA content of the cell [3] while transcriptomics relates to study of transcriptomes and their functions. ... The transcriptome analysis of CC indicated a variable expression of LH/hCGR among the patients and intrapatients. LH/hCGR mRNA ... 23] compared the transcriptome profiles of cumulus cells isolated from in vivo and in vitro matured COC at different nuclear ... G. Vigone, V. Merico, A. Prigione et al., "Transcriptome based identification of mouse cumulus cell markers that predict the ...
UTMOST (unified test for molecular signatures) is a method for cross-tissue gene expression imputation for transcriptome-wide ... Transcriptome-wide association analysis is a powerful approach to studying the genetic architecture of complex traits. A key ... Hu, Y., Li, M., Lu, Q. et al. A statistical framework for cross-tissue transcriptome-wide association analysis. Nat Genet 51, ... Transcriptome-wide association analysis is a powerful approach to studying the genetic architecture of complex traits. A key ...
Digital transcriptome subtraction (DTS) is a bioinformatics method to detect the presence of novel pathogen transcripts through ... Feng H, Taylor JL, Benos PV, Newton R, Waddell K, Lucas SB, Chang Y, Moore PS (August 2007). "Human Transcriptome Subtraction ... Must have a highly reliable, complete reference transcriptome for the organism being studied. Lack of foreign sequence ... "New Pathogen Discovery: Digital Transcriptome Subtraction". Archived from the original on 25 January 2010. Retrieved 1 March ...
... *Download PDF Copy ... The transcriptome data indicates multiple stress-responsive genes such as C2H2 and Myb gene families. Together, it provides ... R. Sowdhamini at the National Centre for Biological Sciences (NCBS), Bengaluru, has recently deciphered the transcriptome by ...
Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of cDNA ... Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of cDNA ... title = {Alternative isoform regulation in human tissue transcriptomes},. journal = {Nature},. year = {2008},. pages = {470-- ...
Thank you for your interest in spreading the word about Science.. NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.. ...
Overlapping Airway Basal Cell Transcriptome Reprogramming in COPD and Lung Cancer. * Share ...
In this work, we developed transcriptome post-scaffolding (TransPS) to scaffold preassembled transcriptome from any desired ... nonredundant de novo transcriptomes. TransPS shows promising results on the test transcriptome datasets, where redundancy is ... A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs. Mingming Liu,1 Zach N. Adelman,2 Kevin M. Myles,2 ... Widely used transcriptome assembly tools include Cufflinks [2] for reference based assembly and Trinity [3] and Oases [4] for ...
2. Construction of Transcriptome Sequencing Library. When performing transcriptome sequencing, the total RNA in the sample is ... The transcriptome data is mainly derived from the exon sequence of the genome. The transcriptome reads obtained by sequencing ... Single-cell transcriptome sequencing technology is a technique to study the entire transcriptome at the single-cell level. It ... Through the whole transcriptome data, not only the expression profiles of all types of transcripts can be obtained, on this ...
... Nature. 2010 Mar 11;464(7286):250-5. doi: 10.1038/ ... Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species. ...
Date: 2019-09-26, Time: 15:00:00, Speaker: Heather Hundley, Location: IMP Lecture Hall, Type: DK RNA Biology Seminar, Institute: Indiana University School of Medicine, Host: Michael Jantsch ...
  • Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being actively expressed at any given time, with the exception of mRNA degradation phenomena such as transcriptional attenuation . (wikipedia.org)
  • In accordance with the central dogma of molecular biology, the transcriptome initially encompassed only protein-coding mRNA transcripts. (wikipedia.org)
  • The transcriptome is the full set of messenger RNA (mRNA) a cell has transcribed. (news-medical.net)
  • Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of cDNA fragments, yielding a digital inventory of gene and mRNA isoform expression. (psu.edu)
  • Sequence assembly approaches have been modified to meet the requirements for de novo transcriptomes, which have complications not found in traditional genome assemblies such as variation in coverage for each candidate mRNA and alternative splicing. (hindawi.com)
  • Whole transcriptome sequencing can determine all complete transcripts in a sample, including mRNA and non-coding RNA (lncRNA, circRNA and miRNA). (selfgrowth.com)
  • The whole transcriptome sequencing requires the establishment of 2 libraries (mRNA + lncRNA + circRNA library and miRNA library) or 3 libraries (mRNA + lncRNA library, circRNA library and miRNA library) during the library construction process. (selfgrowth.com)
  • First works on transcriptome analysis in fruit tree species started at the mRNA level in the early 2000s with cDNA-AFLP (cDNA Amplified Fragment Length Polymorphism) analysis, the development of ESTs (expressed sequence tags) and the analysis of several candidate genes. (frontiersin.org)
  • One of these systems is massive transcriptome analysis using cDNA biochips (microarrays) to analyze thousands of genes by hybridization of mRNA labeled with fluorescence. (frontiersin.org)
  • We analyzed the mRNA and miRNA transcriptomes of human neuronal stem cells (hNSCs) during infection with ZIKV MR766 and Paraiba strains. (medworm.com)
  • The other approach, de novo transcriptome assembly , uses software to infer transcripts directly from short sequence reads. (wikipedia.org)
  • In this work we proposed TransPS, a transcriptome post-scaffolding method, to generate high quality, nonredundant de novo transcriptomes. (hindawi.com)
  • There are three typical transcriptome assembly strategies: the reference based strategy, the de novo strategy, and the hybrid strategy that combines both reference based and de novo strategies. (hindawi.com)
  • Scaffolding translation mapping (STM) [ 6 ] is an optimization method of de novo transcriptome assembly by scaffolding contigs and reads. (hindawi.com)
  • When using transcriptome data for de novo stitching, it helps to demarcate the boundaries of transcripts and determine the sense chain information of transcripts. (selfgrowth.com)
  • In this work, we present a comprehensive de novo transcriptome assembly of C. tiglium based on a normalized library to cover a huge variety of transcripts. (frontiersin.org)
  • The garlic transcriptome has been de novo assembled by several previous studies, and large numbers of expressed genes have been discovered [17, 18]. (thefreelibrary.com)
  • By combining NuGEN's amplification technology with 454 Sequencing Systems, we provide a solution that meets these researchers' needs, while allowing them to leverage the power of 454 Sequencing System's long read lengths which are critical for both de novo transcriptome assembly and comprehensive identification of splice variants and fusion transcripts. (fiercebiotech.com)
  • The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. (wikipedia.org)
  • One NGS technique used to characterize transcriptome is cDNA sequencing. (news-medical.net)
  • We developed a microfluidic approach to prepare cDNA from single cells for high-throughput transcriptome sequencing. (pnas.org)
  • High-throughput sequencing of RNA (RNA-Seq), based on lowering the costs of DNA sequencing (in this case complementary, cDNA), makes it possible to obtain nearly the complete characterization of transcriptomic events occurring in a specific tissue or plant and represents the latest and most powerful tool for characterizing transcriptomes. (frontiersin.org)
  • 2003) Targeting a complex transcriptome: the construction of the mouse full‐length cDNA encyclopedia. (els.net)
  • 2005) Dissection of the inflammatory bowel disease transcriptome using genome‐wide cDNA microarrays. (els.net)
  • The set of genes which are transcribed in any one condition is known as the transcriptome, and the process of determining the genetic codes contained in the transcriptome, and their relative proportions, is known as transcriptome sequencing. (warwick.ac.uk)
  • Attempts to characterize the transcriptome became more prominent with the advent of automated DNA sequencing during the 1980s. (wikipedia.org)
  • RNA sequencing of single cells enables measurement of biological variation in heterogeneous cellular populations and dissection of transcriptome complexity that is masked in ensemble measurements of gene expression. (pnas.org)
  • Many techniques have, thus, been recently developed to perform transcriptome sequencing (RNA-Seq) on individual cells. (pnas.org)
  • Transcriptome sequencing (RNA-Seq) is a recently developed technology that uses high-throughput sequencing approaches (next-generation sequencing or NGS) to determine the sequence of all RNA transcripts in a given specimen. (springer.com)
  • Applications of new sequencing technologies for transcriptome analysis. (springer.com)
  • Malone JH, Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome. (springer.com)
  • Tenders are invited for Towards transcriptome sequencing and analysis of drought induced plant leaf and root samples. (thefreedictionary.com)
  • The quality of RNA preparations used for transcriptome sequencing was examined (Table 2). (thefreedictionary.com)
  • Accurate and reproducible RNA transcriptome analysis has traditionally been challenging for next generation sequencing platforms due to errors associated with reverse transcription, amplification, and manipulations during library preparation, particularly for low input samples and single cells. (thefreedictionary.com)
  • In a collection of articles published by BioMed Central, including a lead article in Genome Biology, the Australian-led, international Tammar Wallaby Genome Sequencing Consortium present the tammar wallaby genome and transcriptome sequences. (biomedcentral.com)
  • In this volume, Dr. Pyo Hong discusses the role of long RNA sequences in transcriptome analysis, Dr. Shinichi describes the next-generation single-cell sequencing technology developed by his team, Dr. Prasanta presents transcriptome analysis applied to rice under various environmental factors, Dr. Xiangyuan addresses the reproductive systems of flowering plants and Dr. Sadovsky compares codon usage in conifers. (intechopen.com)
  • With the rapid development of high throughput sequencing technologies, new transcriptomes can be sequenced for little cost with high coverage. (hindawi.com)
  • However, transcriptome assembly is even more difficult than genome assembly due to the complication of factors such as highly variable sequencing depth, strand specificity, and transcript variants [ 1 ]. (hindawi.com)
  • Single-cell transcriptome sequencing technology is a technique to study the entire transcriptome at the single-cell level. (selfgrowth.com)
  • Unlike other RNA sequencing technologies, scRNA-seq needs to first isolate and obtain all transcriptomes within a single cell. (selfgrowth.com)
  • When performing transcriptome sequencing, the total RNA in the sample is extracted, rRNA is removed, and the target sequencing RNA molecule is enriched to construct a sequencing library. (selfgrowth.com)
  • In transcriptome sequencing, distinguishing the source of RNA molecular chains can avoid the interference of reads on the antisense strand of genes, and can improve the accuracy of gene transcript identification and transcript quantification. (selfgrowth.com)
  • The Ion Proton System, combined with Ambion RNA kits, delivers fast, flexible, and high-quality transcriptome sequencing at an affordable price. (thermofisher.com)
  • However, the recent sequencing of the complete genome of different tree fruit species including apple, peach or Japanese apricot, together with the availability of new high-throughput sequencing ("deep-sequencing") technologies, is offering new possibilities for fruit tree transcriptome analysis. (frontiersin.org)
  • I will then continue to describe my recent and ongoing algorithmic work on clustering, error correction, and alignment of long-read transcriptome sequencing data. (kth.se)
  • Illumina offers comprehensive next-generation sequencing (NGS) solutions that provide high-quality gene expression and transcriptome analysis data for a broad range of sample types. (illumina.com)
  • Why the PacBio® System for Transcriptome Sequencing? (speakerdeck.com)
  • We used RNA sequencing (RNA-seq) to obtain the transcriptomes of isolated lupulin glands, cones with glands removed and leaves from high alpha-acid hop cultivars, and analyzed these datasets for genes involved in bitter acid biosynthesis including the supply of major precursors. (7thspace.com)
  • As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages, and compared these with transcriptomes of diverse vegetative tissues, including leaves, roots, and stems. (csir.co.za)
  • In this study, the global gene expression profiling of P. aeruginosa strain PA-99 and P. aeruginosa CGMCC1.2620 (PA1.2620) was conducted using transcriptome sequencing. (dovepress.com)
  • Transcriptome sequencing detected 672 upregulated and 787 downregulated genes, covering Clusters of Orthologous Groups (COGs) of P. aeruginosa strain PA-99 compared with PA1.2620. (dovepress.com)
  • Together with 454 Sequencing Systems, the research community can perform whole transcriptome profiling on samples with as little as 500 pg of total RNA. (fiercebiotech.com)
  • Here, we sample from the developmental time course of diapause in both strains and use transcriptome sequencing to profile regulatory and amino acid changes associated with timing divergence. (biologists.org)
  • Since the transcripts are the products of transcribed or 'active' genes we can also use this sequence information in multiple sequence alignments using transcriptome sequence from different individuals - for example the parents of a mapping population. (warwick.ac.uk)
  • The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. (wikipedia.org)
  • The first seminal study to mention and investigate the transcriptome of an organism was published in 1997 and it described 60,633 transcripts expressed in S. cerevisiae using serial analysis of gene expression (SAGE). (wikipedia.org)
  • The transcriptome encompasses all the ribonucleic acid (RNA) transcripts present in a given organism or experimental sample. (wikipedia.org)
  • The transcriptome is the entire assembly of RNA transcripts in a given cell type, including protein coding and noncoding transcripts. (springer.com)
  • Digital transcriptome subtraction (DTS) is a bioinformatics method to detect the presence of novel pathogen transcripts through computational removal of the host sequences. (wikipedia.org)
  • Subtracted sequences typically include: Reference human transcriptome - eliminates any known human transcripts from expression library sets. (wikipedia.org)
  • Transcriptome analysis is the study of the transcriptome, of the complete set of RNA transcripts that are produced under specific circumstances, using high-throughput methods. (intechopen.com)
  • Through the whole transcriptome data, not only the expression profiles of all types of transcripts can be obtained, on this basis, different RNA molecules are identified and annotated, their encoded proteins and regulatory functions are analyzed, and the interaction between RNA molecules is regulated Network analysis, comprehensively and systematically analyze the biological characteristics of specific cells in a specific time and space. (selfgrowth.com)
  • We developed a high resolution transcriptome (HRT) method to determine the full repertoire of transcripts in neural stem cells, migrating neurons, and differentiating neurons. (yale.edu)
  • RESULTS: Luteolin dose-dependently suppressed pro-inflammatory marker expression in LPS-activated microglia and triggered global changes in the microglial transcriptome with more than 50 differentially expressed transcripts. (greenmedinfo.com)
  • Transcriptome analysis experiments can characterize transcriptional activity (coding and non-coding), focus on a subset of relevant target genes and transcripts, or profile thousands of genes at once to create a global picture of cell function. (illumina.com)
  • Discover alternative transcripts, gene fusions, and allele-specific expression patterns with a clear, complete view of the coding transcriptome. (illumina.com)
  • The objective of this study was to develop an understanding of the amniotic fluid core transcriptome by analyzing the transcripts ubiquitously present in the amniotic fluid supernatant of euploid midtrimester fetuses. (lww.com)
  • Transcripts are often like a recipe for making proteins, and a collection of all the transcripts in a cell is called a transcriptome. (innovations-report.com)
  • A number of organism-specific transcriptome databases have been constructed and annotated to aid in the identification of genes that are differentially expressed in distinct cell populations. (wikipedia.org)
  • Once a transcriptome has been sequenced, we can use the information to identify which parts of the genome are used to code for active genes. (warwick.ac.uk)
  • If several transcriptomes have been sequenced under different growth or environmental conditions, we can start to estimate which genes are more important in which biological processes. (warwick.ac.uk)
  • These limitations have restricted analysis of all genes in a large genome and detection of uncommon but physiologically relevant genes in the transcriptome. (news-medical.net)
  • The finding and annotating of the transcriptome in tissues elucidates which genes are being expressed, and their tentative function. (news-medical.net)
  • Thus, clonal heterogeneity of gene expression level is not due to independent noise in the expression of individual genes, but reflects metastable states of a slowly fluctuating transcriptome that is distinct in individual cells and may govern the reversible, stochastic priming of multipotent progenitor cells in cell fate decision. (nature.com)
  • The transcriptome data indicates multiple stress-responsive genes such as C2H2 and Myb gene families. (news-medical.net)
  • We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. (springer.com)
  • There are about 60,000 long noncoding RNA genes in the human genome, or about three times more than coding RNA, and this number continues to grow as we learn more about the transcriptome. (fluidigm.com)
  • Therefore, our comprehensive analysis of dynamic synovial transcriptomes provides previously unidentified antiarthritic genes, Itgb1, Rps3, and Ywhaz, which can serve as molecular markers to predict disease remission, as well as therapeutic targets for chronic inflammatory arthritis. (jci.org)
  • More recently, new strategies of massive analysis (high-throughput) of transcriptomes have been applied, producing larger amounts of data in terms of expression of a large number of genes in a single experiment. (frontiersin.org)
  • Here we show that a CBE with rat APOBEC1 can cause extensive transcriptome-wide deamination of RNA cytosines in human cells, inducing tens of thousands of C-to-U edits with frequencies ranging from 0.07% to 100% in 38-58% of expressed genes. (massgeneral.org)
  • A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer. (kb.se)
  • The assembly of gene-specific data concerning the male gametophytic transcriptome has revealed approximately 150 different genes, assigned to 16 distinct function groups, with strong evidence for pollen-specific expression in about 30 ( Twell, 2002 ). (plantphysiol.org)
  • Together, the transcriptome and genome can be used as a reference for pinpointing differences in slender false brome genes and gene activity that may contribute to its invasive capabilities. (innovations-report.com)
  • To allow future studies to identify the functions of slender false brome genes, the authors also compared the false brome transcriptome to those of well-studied agricultural species, including rice and sorghum. (innovations-report.com)
  • Tariq RanaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-seq was utilized to characterize the transcriptome of human neural stem cells infected with Zika virus strains MR766 and Paraiba at MOI 1. (medworm.com)
  • For these reasons, the aim of this work is to characterize the transcriptome of soybean line PI 595099- Meloidogyne javanica interaction through expression analysis. (scielo.br)
  • RNA-seq is emerging (2013) as the method of choice for measuring transcriptomes of organisms, though the older technique of DNA microarrays is still used. (wikipedia.org)
  • Subsequently, the advent of high-throughput technology led to faster and more efficient ways of obtaining data about the transcriptome. (wikipedia.org)
  • Although single-cell transcriptome analyses from various biopsied tissues have been published recently, corresponding protocols for human endometrium have not been described. (nih.gov)
  • The frozen-thawed endometrial biopsies were fluorescence-activated cell sorted (FACS) to distinguish CD13-positive stromal and CD9-positive epithelial cells and single-cell transcriptome analysis performed from biopsied tissues without culturing the cells. (nih.gov)
  • Quantitative analysis of biomolecular networks and regulatory pathways in cells or specific tissues in a certain space-time requires quantitative and qualitative research on all RNA molecules in the entire transcriptome. (selfgrowth.com)
  • Two biological techniques are used to study the transcriptome, namely DNA microarray, a hybridization-based technique and RNA-seq, a sequence-based approach. (wikipedia.org)
  • To explore the cross talk between the glycome and the transcriptome during vasculogenesis, we identified by microarray and then validated wild-type and NDST1 knockdown-associated gene-expression patterns in zebrafish embryos. (ahajournals.org)
  • Microarray analysis continues to be one of the most important approaches for transcriptome analysis in fruit trees. (frontiersin.org)
  • We present a genome-wide view of the male gametophytic transcriptome in Arabidopsis based on microarray analysis. (plantphysiol.org)
  • Harbers M, Carninci P. Tag-based approaches for transcriptome research and genome annotation. (springer.com)
  • Transcription profiling, which follows total changes in the behavior of a cell, is used throughout diverse areas of biomedical research, including diagnosis of disease, biomarker discovery, risk assessment of new drugs or en. (intechopen.com)
  • This webinar will outline a project that performs large-scale and integrative single-cell genome and transcriptome profiling of pediatric acute lymphoblastic leukemia (ALL) cases at diagnosis, during drug treatment, and in case of relapse. (genomeweb.com)
  • Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. (springer.com)
  • Perform transcriptome profiling for hundreds to tens of thousands of single cells in one experiment. (illumina.com)
  • Are you interested in starting a new transcriptome profiling project? (thermofisher.com)
  • Transcriptome analysis by NGS is rapid, inexpensive, and unlimited by genomic complexity and has been widely used as a primary tool in many researching areas, including gene discovery, SSR marker development, and investigation of the domesticated patterns of crops, particularly in the characterization of the gene expression profiling [14-16]. (thefreelibrary.com)
  • In this study, to detect the potential mechanism of garlic discoloration caused by low-temperature stress, three low-temperature-treated garlic samples with different times which resulted in different degrees in discoloration and control garlic were exploited for genome-wide transcriptome profiling analysis. (thefreelibrary.com)
  • This collaborative effort provides researchers an end-to-end solution for transcriptome profiling using their most precious sample types. (fiercebiotech.com)
  • however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. (mcponline.org)
  • Mechanism-Of-Action Classification of Antibiotics by Global Transcriptome Profiling. (jcvi.org)
  • In the present study, we re-assembled the transcriptome datasets of B. (thefreedictionary.com)
  • TransPS shows promising results on the test transcriptome datasets, where redundancy is greatly reduced by more than 50% and, at the same time, coverage is improved considerably. (hindawi.com)
  • The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics. (springer.com)
  • Popular brain transcriptome methods are powerful at detecting global gene expression. (yale.edu)
  • Brain Transcriptome Edition by Hitzemann, Robert and Publisher Academic Press. (vitalsource.com)
  • When combined with laser-directed microdissection, intact RNA from unfixed, freeze-dried sections can be isolated, which is a prerequisite for high-quality global transcriptome analysis. (jneurosci.org)
  • To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. (usda.gov)
  • As with short read genome assembly, transcriptome assembly needs to connect short and sometimes low quality reads. (hindawi.com)
  • There are two general methods of inferring transcriptome sequences. (wikipedia.org)
  • One approach maps sequence reads onto a reference genome, either of the organism itself (whose transcriptome is being studied) or of a closely related species. (wikipedia.org)
  • The purpose of this study was to test the hypothesis that the Saccharomyces cerevisiae transcriptome might be used as an indicator of phytochemical variation of closely-related yet distinctly different extracts prepared from a single species of a phytogeographically widely distributed medicinal plant. (scoop.it)
  • In this work, we developed transcriptome post-scaffolding (TransPS) to scaffold preassembled transcriptome from any desired assembler using a reference species to improve transcriptome coverage and reduce config redundancy. (hindawi.com)
  • Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species. (nih.gov)
  • The transcriptome can be described in plants, including in fruit tree species, as the complete list of all types of RNA molecules expressed in a cell, tissue or whole organism. (frontiersin.org)
  • We now know that this `transcriptome' is unexpectedly complex and its precise definition in any one species requires multiple technical approaches and an ability to work on a very large scale. (biologists.org)
  • These samples of messenger RNA were suitably mixed to ensure that most of the transcriptome of the species would be found in the overall sample. (thefishsite.com)
  • The transcriptome provides an extensive genetic tool for studying how invasive species, like slender false brome, successfully spread into novel ranges. (innovations-report.com)
  • Analysis of the transcriptomes of human oocytes and embryos is used to understand the molecular mechanisms and signaling pathways controlling early embryonic development, and could theoretically be a powerful tool in making proper embryo selection in in vitro fertilisation . (wikipedia.org)
  • Data obtained from the transcriptome is used in research to gain insight into processes such as cellular differentiation, carcinogenesis, transcription regulation and biomarker discovery among others. (wikipedia.org)
  • The extent of the Pol III transcriptome, the complexity of its regulation and its influence on cell physiology, development and disease are emerging as new areas for future research. (nih.gov)
  • General schema showing the relationships of the genome , transcriptome , proteome , and metabolome ( lipidome ). (wikipedia.org)
  • The transcriptome can be seen as a subset of the proteome , that is, the entire set of proteins expressed by a genome. (wikipedia.org)
  • As such, transcriptome and transcriptomics were one of the first words to emerge along with genome and proteome. (wikipedia.org)
  • To explore the influence of ADAT activity on mammalian translation, we have characterized the human transcriptome and proteome in terms of frequency and distribution of ADAT-related codons. (mdpi.com)
  • Transcriptome dynamics at Arabidopsis graft jun. (scoop.it)
  • By characterizing the transcriptome patterns and pathways for these symptoms, our goal is to shed light on the biological mechanisms underlying this comorbidity, which can help prevent the exacerbation of physical symptoms by intervening at the level of etiological pathway. (cdc.gov)
  • Transcriptome analysis showed separation of CD19+ and CD19- subsets that included pathways such as cell cycle, hypoxia, TNF-α, and unfolded protein response. (jcvi.org)
  • The transcriptome is the set of all RNA molecules in one cell or a population of cells . (wikipedia.org)
  • Transcriptome-obtained data also finds applications in establishing phylogenetic relationships during the process of evolution and in in vitro fertilization. (wikipedia.org)
  • In this study, we obtained a batch of simple sequence repeats (SSRs) from the transcriptome data of Asian moon scallop Amusium pleuronectes and analyzed the distribution and frequency of these SSRs. (thefreedictionary.com)
  • They have been rarely studied at the genetic level most likely due to the lack of genomic and transcriptome data. (thefreedictionary.com)
  • The data show a unique signature in the Pseudomonas aeruginosa transcriptome in response to perturbation of outer membrane biogenesis. (asm.org)
  • Now you can explore our transcriptome data on the UCSC genome browser. (yale.edu)
  • This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. (bioconductor.org)
  • In order to compare 'digital transcriptome' data, they have to be normalized or adjusted to a common standard of measurement. (systemsbiology.org)
  • In a paper ( Optimal Scaling of Digtial Transcriptomes ) published today in PLOS ONE, researchers at ISB compare several methods currently used to normalize gene expression data and describe new algorithms developed at ISB that outperform commonly used normalization methods. (systemsbiology.org)
  • At the Eurotox meeting in Seville, Marcel Leist held the Bo Helmstedt memorial lecture "Assessment of functional impairment and transcriptome changes based on human stem cell derived developmental toxicity tests" on September 6. (thefreedictionary.com)
  • Celine Everaert, another doctoral fellow in the lab, noted, "The deeper we look into the human transcriptome, the more of these overlapping sense and antisense gene pairs we observe. (fluidigm.com)
  • We conducted a transcriptome-wide association study (TWAS) of triglycerides (TG), HDL cholesterol (HDL-C), LDL cholesterol (LDL-C), and total cholesterol (TC) using whole blood derived RNA from 1,838 Framingham Heart Study participants using the Affymetrix GeneChip Human Exon 1.0 ST array. (ahajournals.org)
  • Differential transcriptome and development of human peripheral plasma cell subsets. (jcvi.org)
  • Discover novel gene isoforms, profile gene expression for select targets of interest, analyze the whole coding transcriptome, and accurately perform transcript abundance and fold-change measurement. (illumina.com)
  • What is a Transcriptome Sequence? (warwick.ac.uk)
  • In this talk, I will present my research on algorithms to reduce the computational bottleneck in some common bioinformatic problems encountered in genome and transcriptome sequence analysis. (kth.se)
  • 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)
  • The TransPlex Whole Transcriptome Amplification ( WTA1 ) and the Complete Whole Transcriptome Amplification Kit ( WTA2 ) provide an accurate, fast and simple method of amplifying total RNA from a variety of sources including blood, fixed and frozen tissue, cell culture, FACS sorted cells, plants and microorganisms. (sigmaaldrich.com)
  • The WTA technology accurately amplifies total RNA by the utilization of a unique blend of quasi-random primers to ensure accurate transcriptome coverage and rapid amplification of total RNA. (sigmaaldrich.com)
  • However, in this study, transcriptome analysis was performed after varicocelectomy and only in patients with MA. (thefreedictionary.com)
  • How can we study the full transcriptome of endometrial stromal and epithelial cells at the single-cell level? (nih.gov)
  • Transcriptome is the RNA content of the cell [ 3 ] while transcriptomics relates to study of transcriptomes and their functions. (hindawi.com)
  • The present study elucidates the potential coregulation of vasculogenesis by the heparan sulfate glycosaminoglycan-rich cell-surface glycome and the transcriptome. (ahajournals.org)
  • Conclusions- The present study for the first time implicates interplay between the glycome and the transcriptome during vasculogenesis, revealing the possibility of harnessing specific cellular glyco-microenvironments for therapeutic vascularization. (ahajournals.org)
  • Here, we evaluated mouse models of age-associated memory impairment and amyloid deposition to study transcriptome and cell type-specific epigenome plasticity in the brain and peripheral organs. (jci.org)
  • This study provides a systems-level investigation of transcriptome plasticity in the hippocampal CA1 region in aging and AD models and suggests that histone deacetylase inhibitors should be further explored as a cost-effective therapeutic strategy against age-associated cognitive decline. (jci.org)
  • To facilitate the drug discovery processes, we present a large-scale study of reference antibiotic challenge bacterial transcriptome profiles which included 37 antibiotics across 6 mechanisms of actions (MOAs) and provide an economical approach to aid in antimicrobial dereplication in the discovery process. (jcvi.org)
  • Cell Ranger (updated): analysis pipelines that combine robust transcriptome alignment with cellular barcoding to rapidly generate expression profiles across tens of thousands of cells at once, now automatically generates Loupe Cell Browser-ready files for both single-sample and multi-sample experiments. (thefreedictionary.com)
  • The core SMART technology has been modified in this kit to generate complete transcriptome coverage of both coding and non-coding RNA while incorporating indexes and adapters in the workflow, which eliminates the need for a downstream library preparation kit. (clontech.com)
  • For the upcoming year the challenge for the UPV/EHU research team to decode the transcriptome of the slug in order to generate a health profile of the soil. (thefishsite.com)
  • Conclusions: Our analysis of the hop transcriptome significantly expands the genomic resources available for this agriculturally-important crop. (7thspace.com)
  • These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects. (plos.org)
  • Our methods can normalize digital transcriptomes without relying on either. (systemsbiology.org)
  • Tissue-specific transcriptome analysis via NGS technology has been attempted on a number of organisms of varying complexity. (news-medical.net)
  • In comparison with the transcriptome of the sporophyte throughout development, the pollen transcriptome showed reduced complexity and a unique composition. (plantphysiol.org)
  • Single-cell whole-transcriptome analysis is a powerful tool for quantifying gene expression heterogeneity in populations of cells. (pnas.org)
  • We adapted a previously developed strategy for single-cell RNA-Seq that has shown promise for superior sensitivity and implemented the chemistry in a microfluidic platform for single-cell whole-transcriptome analysis. (pnas.org)
  • In recent years, innovative technologies for single-cell genomics, transcriptomics, and proteomics, with a particular emphasis on quantification and multiplicity that can perform measurements on many single cells in a given experimental run, include microfluidics, optical tweezers, transcriptome in vivo analysis, and mass cytometry [4,8-10]. (thefreedictionary.com)
  • Single-cell transcriptome analysis of endometrial tissue. (nih.gov)
  • NEW YORK (GenomeWeb) - Researchers have constructed a single-cell transcriptome atlas showing network changes that occur during the progression from precancerous lesions to early gastric cancer. (genomeweb.com)
  • We define circulating-ASC heterogeneity in vaccine responses using multicolor flow cytometry, morphology, VH repertoire, and RNA transcriptome analysis. (jcvi.org)
  • The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the processes of cellular differentiation and carcinogenesis . (wikipedia.org)
  • The responses by the transcriptome to dietary restriction have been studied at the cellular and organismal level, but only recently at a tissue level. (news-medical.net)
  • The analyzed transcriptome provides the 1805 DEGs and gene networks involving cellular processes. (thefreedictionary.com)
  • Unlike the genome , which is roughly fixed for a given cell line (excluding mutations ), the transcriptome can vary with external environmental conditions. (wikipedia.org)
  • The transcriptome can give us information about what the cell is actively doing or will do in the future. (news-medical.net)
  • In 2007, the term "Digital Transcriptome Subtraction" was coined by the Chang-Moore group, and was used to discover Merkel cell polymavirus in Merkel cell carcinoma. (wikipedia.org)
  • OBJECTIVE- To document the transcriptome of the pancreatic islet during the early and late development of the mouse pancreas and highlight the qualitative and quantitative features of gene expression that contribute to the specification, growth, and differentiation of the major endocrine cell types. (diabetesjournals.org)
  • Analysis of the functional composition of the pollen transcriptome revealed the over-representation of mRNAs encoding proteins involved in cell wall metabolism, cytoskeleton, and signaling and under-representation of mRNAs involved in transcription and protein synthesis. (plantphysiol.org)
  • SPAIN - The Cell Biology in Environmental Toxicology research team at the Department of Zoology and Animal Cell Biology at the University of the Basque Country (UPV/EHU) has decoded the transcriptome for the grey mullet. (thefishsite.com)
  • The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at ten different developmental and infection stages based on a 3′-tag digital gene-expression protocol. (apsnet.org)
  • Clonal heterogeneity of Sca-1 expression reflects transcriptome-wide noise. (nature.com)
  • RNA-Seq provides a unique combination of transcriptome-wide coverage, sensitivity, and accuracy for a comprehensive view of gene expression changes. (illumina.com)
  • As a direct result, the development and commercialization of an ever‐increasing number of sensitive tools to measure global gene expression (the 'transcriptome') is providing unique opportunities to evaluate and compare biological systems. (els.net)
  • We observe that deviation from balanced biallelic expression is common, occurring in ∼20% of the mouse transcriptome in a given tissue. (genetics.org)
  • gene expression, root knot nematode, transcriptome. (scielo.br)
  • Pour cela, nous avons utilisé des approches classiques de toxicologie et mis en place une technique d'analyse globale: SAGE (Serial Analysis of Gene Expression). (irsn.fr)
  • Comparing transcriptomes across ranges will reveal new changes in gene expression in the highly successful invasive population. (innovations-report.com)
  • Fox and colleagues have assembled the transcriptomes for two slender false brome populations from its native range (Greece, Spain) and one population from its invasive range (Oregon). (innovations-report.com)
  • The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. (plos.org)
  • Functional analysis identified six physiologic systems represented in the amniotic fluid core transcriptome, including musculoskeletal and nervous system development and function and embryonic and organismal development. (lww.com)