Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Oligonucleotide Array Sequence Analysis: 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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.High-Throughput Nucleotide Sequencing: 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.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Gene Library: 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.Gene Ontology: 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.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Cluster Analysis: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Genes, Plant: The functional hereditary units of PLANTS.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Messenger: 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, Genetic: Databases devoted to knowledge about specific genes and gene products.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Computational Biology: 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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Proteome: The protein complement of an organism coded for by its genome.Gene Regulatory Networks: 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.Reverse Transcriptase Polymerase Chain Reaction: 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.Gene Expression Regulation: 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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Stress, Physiological: 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.Arabidopsis: 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.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Plant Roots: 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)Molecular Sequence Data: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Gene Expression Regulation, Developmental: 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.Reproducibility of Results: 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.Alternative Splicing: 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.DNA, Complementary: 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.Plant Leaves: 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)Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.RNA, Untranslated: 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.RNA: 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)Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Signal Transduction: 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.RNA Isoforms: The different gene transcripts generated from a single gene by RNA EDITING or ALTERNATIVE SPLICING of RNA PRECURSORS.Metabolome: The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.MicroRNAs: 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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Flowers: The reproductive organs of plants.Biosynthetic Pathways: Sets of enzymatic reactions occurring in organisms and that form biochemicals by making new covalent bonds.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Genome, Human: 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.Cicer: A plant genus of the family FABACEAE known for the edible beans.Microsatellite Repeats: 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).Species Specificity: 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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Multigene Family: 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)Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Regulon: 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.Models, Genetic: 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.Host-Pathogen Interactions: The interactions between a host and a pathogen, usually resulting in disease.RNA, Antisense: 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.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.Databases, Nucleic Acid: 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.Oryza sativa: 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.Open Reading Frames: 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).Plant Diseases: Diseases of plants.Exons: 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.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.RNA, Small Untranslated: Short RNA, about 200 base pairs in length or shorter, that does not code for protein.Droughts: Prolonged dry periods in natural climate cycle. They are slow-onset phenomena caused by rainfall deficit combined with other predisposing factors.Secondary Metabolism: A physiochemical process which occurs in a wide range of organisms which unlike BASAL METABOLISM is not required for or essential to short-term survivability but to long-term general well-being of the organism.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Bacterial Proteins: Proteins found in any species of bacterium.Gossypium: A plant genus of the family MALVACEAE. It is the source of COTTON FIBER; COTTONSEED OIL, which is used for cooking, and GOSSYPOL. The economically important cotton crop is a major user of agricultural PESTICIDES.Laser Capture Microdissection: 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.Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.Salinity: 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.Insect Proteins: Proteins found in any species of insect.Genes, Insect: The functional hereditary units of INSECTS.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Up-Regulation: 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.Hemiptera: 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.Gene Fusion: 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.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Mutation: 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.Adaptation, Physiological: The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.Fruiting Bodies, Fungal: The fruiting 'heads' or 'caps' of FUNGI, which as a food item are familiarly known as MUSHROOMS, that contain the FUNGAL SPORES.Tracheobionta: A subset of various vascular plants (also known as the Tracheophyta) which include seed-bearing and non seed-bearing species.Plant Growth Regulators: 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.Populus: 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.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Seedling: Very young plant after GERMINATION of SEEDS.Nucleotide Motifs: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Seeds: 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.RNA, Helminth: Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.Symbiosis: 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.Down-Regulation: 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.Fish Proteins: Proteins obtained from species of fish (FISHES).RNA Editing: 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).DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Carbohydrate Metabolism: Cellular processes in biosynthesis (anabolism) and degradation (catabolism) of CARBOHYDRATES.RNA Splice Sites: 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.Life Cycle Stages: 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.Cajanus: A plant genus of the family FABACEAE that is used for food in NIGERIA.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Trans-Splicing: 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.Salt-Tolerant Plants: Plants that can grow well in soils that have a high SALINITY.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Disease Resistance: 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.Models, Biological: 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.Root Nodules, Plant: 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.Polymerase Chain Reaction: 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.Mycelium: The body of a fungus which is made up of HYPHAE.RNA Stability: 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.Sequence Analysis: 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.Genetic Variation: Genotypic differences observed among individuals in a population.Genes, Bacterial: The functional hereditary units of BACTERIA.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Biological Processes: Biological activities and function of the whole organism in human, animal, microorgansims, and plants, and of the biosphere.Rana clamitans: 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).Embryonic Stem Cells: 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, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.Cell Line, Tumor: A cell line derived from cultured tumor cells.Acclimatization: Adaptation to a new environment or to a change in the old.Fruit: The fleshy or dry ripened ovary of a plant, enclosing the seed or seeds.Mice, Inbred C57BLZea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.Internet: 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.Nitrogen: 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.Introns: 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.Alu Elements: 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.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Lycopersicon esculentum: A plant species of the family SOLANACEAE, native of South America, widely cultivated for their edible, fleshy, usually red fruit.Microdissection: The performance of dissections with the aid of a microscope.Paracoccidioides: A mitosporic fungal genus. P. brasiliensis (previously Blastomyces brasiliensis) is the etiologic agent of PARACOCCIDIOIDOMYCOSIS.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Saccharum: A plant genus of the family POACEAE widely cultivated in the tropics for the sweet cane that is processed into sugar.Arthropod Antennae: Paired sense organs connected to the anterior segments of ARTHROPODS that help them navigate through the environment.RNA, Long Noncoding: 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.Larva: Wormlike or grublike stage, following the egg in the life cycle of insects, worms, and other metamorphosing animals.Pinus: A plant genus in the family PINACEAE, order Pinales, class Pinopsida, division Coniferophyta. They are evergreen trees mainly in temperate climates.Picrorhiza: 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).Genetic Loci: 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.Hippophae: 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).Polyadenylation: 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, Cultured: 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.Protein Array Analysis: 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.Citrus sinensis: A plant species of the genus CITRUS, family RUTACEAE that provides the familiar orange fruit which is also a source of orange oil.Conserved Sequence: 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.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.Zebrafish: 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.Cunninghamia: A plant genus of the family TAXODIACEAE. Members contain DITERPENES.Pteridium: A plant genus of the family DENNSTAEDTIACEAE. Members contain ptaquiloside, braxin A1, and braxin B. The name is similar to brake fern (PTERIS).Vitis: 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.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Plant Shoots: New immature growth of a plant including stem, leaves, tips of branches, and SEEDLINGS.Oxylipins: 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.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Embryonic Development: Morphological and physiological development of EMBRYOS.Coniferophyta: A plant division of GYMNOSPERMS consisting of cone-bearing trees and shrubs.Comparative Genomic Hybridization: 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.Plant Stems: 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)Pectinidae: 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.Medicago truncatula: 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.Cold Temperature: An absence of warmth or heat or a temperature notably below an accustomed norm.Genes, Mitochondrial: 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.Raphanus: A plant genus of the family BRASSICACEAE known for its peppery red root.Hevea: 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.DNA, Intergenic: 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.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Pseudotsuga: 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.Pycnoporus: A genus of basidiomyceteous fungi in the family POLYPORACEAE. The species all contain bright orange, bracket-like fruiting bodies.Host-Parasite Interactions: 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.Ethylenes: Derivatives of ethylene, a simple organic gas of biological origin with many industrial and biological use.Bambusa: 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.Dinoflagellida: Flagellate EUKARYOTES, found mainly in the oceans. They are characterized by the presence of transverse and longitudinal flagella which propel the organisms in a rotating manner through the water. Dinoflagellida were formerly members of the class Phytomastigophorea under the old five kingdom paradigm.Systems Biology: 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.Pollen: The fertilizing element of plants that contains the male GAMETOPHYTES.Carbon: 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.DNA Primers: 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.Cell Wall: 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.Saccharomyces cerevisiae: 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.Photosynthesis: 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)Xylem: 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.Cyclopentanes: A group of alicyclic hydrocarbons with the general formula R-C5H9.Lignin: 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)Sequence Homology, Nucleic Acid: 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.Arthropod Proteins: 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.Gills: 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.

*  Strand Specific Transcriptome Analysis - Illumina Sequencing

SMARTer Stranded RNA-Seq Kits-Strand-Specific Library Construction for Transcriptome Analysis on Illumina Platforms. The ... The core SMART technology has been modified in this kit to generate complete transcriptome coverage of both coding and non- ...
clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/Next_Gen_Sequencing_Kits/Total_RNA-Seq/Strand-Specific_RNA_Seq_Illumina?sitex=10020:22372:US&PEBCL1=o0y2iLyWOZwUoEJBfxDdbvLlTG&PEBCL1_pses=ZG7952E12C7F002266AA7DF52BF49E87A1E2BADFB4B2EDED769F99C8951ECD644D24F80650DD7C56DCD0634B756FE399B8DF3B9E1B1A9CE8B6

*  Comparative Analysis of Proteome and Transcriptome Variation in Mouse

Transcriptome analysis Is the Subject Area "Transcriptome analysis" applicable to this article? Yes. No. ...
journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1001393

*  Single-cell mRNA-seq-Reproducible, sensitive transcriptome analysis

Transcriptome analysis is an effective way to obtain information regarding the state of a cell or tissue under a wide variety ... Single-Cell Transcriptome Studies: A Powerful Way to Highlight Subtle Differences Between Cells That May Be Hidden in a ... In this study, we looked at the transcriptome of genetically identical individual cells and compared them to each other and to ... This study reinforces the idea that SMART technology can robustly produce cDNA from single cells for meaningful transcriptome ...
clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/NGS_Learning_Resources/Technical_Notes/v4_Single-Cell_mRNA-Seq?sitex=10020:22372:US&PEBCL1=Dm7FTxG1FysZdkrBbUhf5DYMmG&PEBCL1_pses=ZGC4A6FA625F7A680505A469470BE11678F412EBC881A2F2AF1B86A6E123958A18D38BCB6D5BF3FB3075DA61477DCD2CD4A82AFC1EAC80FE84

*  PLOS Genetics: Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture

By leveraging the high resolution of RNA sequencing and broad population sampling, we survey the landscape of transcriptome ...
journals.plos.org/plosgenetics/article/authors?id=10.1371/journal.pgen.1004549

*  DiffSplice: the genome-wide detection of d... [...

Instead, our method takes a divide-and-conquer approach to localize the difference between transcriptomes in the form of ... The availability of high-throughput short-read RNA sequencing technologies provides in-depth sampling of the transcriptome, ... Differential transcription analysis, the detection of differences between the transcriptomes of different cells, may improve ... making it possible to accurately detect the differences between transcriptomes. In this article, we present a new method for ...
scoop.it/t/databases-softwares/p/3508021741/2012/11/28/diffsplice-the-genome-wide-detection-of-d-nucleic-acids-res-2012-pubmed-ncbi

*  Sandwalk: A 2004 kerfuffle over pervasive transcription in the mouse genome

Wang, J., Zhang, J., Zheng, H., Li, J., Liu, D., Li, H., Samudrala, R., Yu, J., and Wong, G.K.-S. (2004) Mouse transcriptome: ... Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely ... The authors set out to define the complete "transcriptome" of the mouse in order to discover new genes. They constructed and ... 2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420:563-573. [doi ...
sandwalk.blogspot.com/2016/03/a-2004-kerfuffle-over-pervasive.html

*  A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog ...

Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to ... Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome ... our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. ... evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. ...
https://peerj.com/articles/3702/

*  Inference from Low Precision Transcriptome Data Representation - ePrints Soton

Tuna, Salih and Niranjan, Mahesan (2010) Inference from Low Precision Transcriptome Data Representation Journal of Signal ...
https://eprints.soton.ac.uk/271193/

*  Review History for Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral...

This is a descriptive study examining the transcriptome changes that occur during a mild H1N1 2009 influenza infection in mice ...
https://peerj.com/articles/3915/reviews/

*  SeedSeq: Off-Target Transcriptome Database

... Shaoli Das,1 Suman Ghosal,1 Jayprokas Chakrabarti,1,2 and Karol Kozak3,4 ... Shaoli Das, Suman Ghosal, Jayprokas Chakrabarti, and Karol Kozak, "SeedSeq: Off-Target Transcriptome Database," BioMed Research ...
https://hindawi.com/journals/bmri/2013/905429/cta/

*  RNA Sequencing Uncovers Complex Maize Transcriptome | GenomeWeb

This webinar will describe a protocol and proof-of-principle experiments for Cellular Indexing of Transcriptome and Epitopes by ... GenomeWeb/ABRF 2017 Webinar Series: CITE-seq: Large-Scale Measurement of Epitopes and Transcriptomes in Single Cells. ...
https://genomeweb.com/sequencing/rna-sequencing-uncovers-complex-maize-transcriptome

*  Transcriptome Yields Two Subtypes of Multiple Sclerosis | GEN

Transcriptome Yields Two Subtypes of Multiple Sclerosis * Scientists have identified two distinct transcription profiles in the ...
https://genengnews.com/gen-news-highlights/transcriptome-yields-two-subtypes-of-multiple-sclerosis/81247392/?kwrd=brigham and women

*  Transplex Whole Transcriptome RNA Amplifications | Sigma-Aldrich

Transplex Whole Transcriptome RNA Amplifications. By: Ken Heuermann, Brian Ward, Biowire Volume 10 Article 1 ... The efficacy of amplification of small quantities of total RNA with the TransPlex® Complete Whole Transcriptome Amplification ... This study confirms that the TransPlex Complete Whole Transcriptome Amplification Kit can effectively amplify low input ... Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process. ...
sigmaaldrich.com/technical-documents/articles/biowire/transplex-whole-transcriptome.html

*  MegaMan Human Transcriptome Library

Genomics , MegaMan Human Transcriptome Library Announcements. * 07/17/2017 Agilent Technologies Introduces New High-Sensitivi ...
genomics.agilent.com/en/Cloning-Libraries/MegaMan-Human-Transcriptome-Library/?cid=AG-PT-114&tabId=AG-PR-1104

*  Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing | SpringerLink

RNA sequencing Single-molecule sequencing Transcriptome profiling Polyadenylation site mapping Springer Nature is developing a ... Ozsolak F., Milos P.M. (2011) Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing. In: Kwon Y., Ricke S. (eds) ... Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes ... Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools ...
https://link.springer.com/protocol/10.1007/978-1-61779-089-8_4

*  "Analysis of the triticeae seed transcriptome" by Peter C...

Analysis of the triticeae seed transcriptome. International Triticeae Mapping Inititative (ITMI) Workshop and the Australian ... Analysis of the triticeae seed transcriptome', paper presented to the International Triticeae Mapping Inititative (ITMI) ...
https://works.bepress.com/toni_paceymiller/97/

*  Improved chemistry for single-cell transcriptome analysis

... SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System. * ... In single-cell transcriptome studies, it is critical to obtain high-quality cDNA libraries from individual cells that represent ... To achieve this, we improved upon our existing commercially available mRNA-seq chemistry for single-cell transcriptome studies ...
clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/NGS_Learning_Resources/Technical_Notes/SMART-Seq-v4-for-Fluidigm-C1?sitex=10020:22372:US&PEBCL1=d9P9UJ8G1DU4v3A88jgf75BP8A&PEBCL1_pses=ZG07AA6B334DEB958FFBCA540064F1BA5529F08BB960C6539E3D5D616F1740DE18F508FB4E90B2BA654623B74F04BF3BD19A0BCD62C1710716

*  Single-Cell cDNA Synthesis For Transcriptome Analysis

SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing-Single-Cell Transcriptome Analysis with Ultimate Sensitivity. The SMART-Seq ... cDNA synthesis from small quantities of cells or total RNA for transcriptome sequencing*cDNA output from this kit can be used ... The core SMART technology in this kit is an immensely powerful tool for studying the full transcriptome, including splice ...
clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/Next_Gen_Sequencing_Kits/Single_cell_RNA_Seq_Kits_for_mRNA_seq/Single_Cell_RNA_Seq_v4?sitex=10020:22372:US&PEBCL1=zZ9MCiyuuFUVIsXPCAandiQHhR&PEBCL1_pses=ZGABFE046105DAAE6D46967E4876CD7E4FF022744BA9D7FD0D5BFAD9C886DF943E4917E74227F37E19B81C555056394B63C2A080C02B7C0384

*  Uncovering the Complexity of Transcriptomes with RNA-Seq

end transcriptome using a next generation DNA sequencer," PLoS ONE, vol. 4, no. 1, article e4108, 2009. View at Publisher · ... Analyzing the transcriptome of organisms without a specific reference genome requires de novo assembling (or a guided assembly ... Uncovering the Complexity of Transcriptomes with RNA-Seq. Valerio Costa,1 Claudia Angelini,2 Italia De Feis,2 and Alfredo ... Indeed, as "transcriptome" is defined as the complete collection of transcribed elements in a genome (see [2]), it consists of ...
https://hindawi.com/journals/bmri/2010/853916/

*  transcriptome analysis of venom glands: post #1

I will like to know why spider venom needs to be extracted a few days before venom gland extraction for transcriptome analysis ... transcriptome analysis of venom glands - posted in -Molecular Biology-: ... transcriptome analysis of venom glands. Started by Ahmed2013, Jan 02 2014 02:41 AM ... I will like to know why spider venom needs to be extracted a few days before venom gland extraction for transcriptome analysis ...
protocol-online.org/forums/topic/31319-transcriptome-analysis-of-venom-glands/

*  Recent Articles | Transcriptome And Culture | The Scientist Magazine®| Page 34

Daily News German Scientists Resign from Elsevier Journals' Editorial Boards These researchers join around 200 research institutions that have cut ties with the publishing giant to support the ongoing push for open access and favorable pricing.. ...
the-scientist.com/?articles.list/tagNo/971,3/tags/transcriptome,culture/pageNo/34/

*  Recent Articles | Transcriptome And Culture | The Scientist Magazine®| Page 1

Some researchers are at risk of job loss and even deportation if Trump decides to end a program that allows undocumented immigrants who arrived in the U.S. as children to obtain work permits. 5 Comments. ...
the-scientist.com/?articles.list/tagNo/971,3/tags/transcriptome,culture/pageNo/1/

*  Recent Articles | Transcriptome, Genetics & Genomics And Ecology | The Scientist Magazine®

tags: transcriptome x genetics & genomics x ecology x disease/medicine x The Scientist. » transcriptome, genetics & genomics, ...
the-scientist.com/?articles.list/categoryNo/2625/category/The-Scientist/tagNo/971,9,7,6/tags/transcriptome,genetics--amp--genomics,ecology,disease-medicine/

De novo transcriptome assembly: De novo transcriptome assembly is the method of creating a transcriptome without the aid of a reference genome.Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?Cellular microarray: A cellular microarray is a laboratory tool that allows for the multiplex interrogation of living cells on the surface of a solid support. The support, sometimes called a "chip", is spotted with varying materials, such as antibodies, proteins, or lipids, which can interact with the cells, leading to their capture on specific spots.Sequence clustering: In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin.Massive parallel sequencing: Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged in 1994-1998 and became commercially available since 2005.Squamosa promoter binding protein: The SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific in vitro binding to the promoter of the snapdragon SQUAMOSA gene.Library (biology): In molecular biology, a library is a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. There are different types of DNA libraries, including cDNA libraries (formed from reverse-transcribed RNA), genomic libraries (formed from genomic DNA) and randomized mutant libraries (formed by de novo gene synthesis where alternative nucleotides or codons are incorporated).Eukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Mature messenger RNA: Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, it consists exclusively of exons, with all introns removed.Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Plant Proteome Database: The Plant Proteome Database is a National Science Foundation-funded project to determine the biological function of each protein in plants.Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ.Biological network: A biological network is any network that applies to biological systems. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole food web.List of sequenced eukaryotic genomesGAI (Arabidopsis thaliana gene)Flux (metabolism): Flux, or metabolic flux is the rate of turnover of molecules through a metabolic pathway. Flux is regulated by the enzymes involved in a pathway.Endodermis: The endodermis is the central, innermost layer of cortex in some land plants. It is made of compact living cells surrounded by an outer ring of endodermal cells that are impregnated with hydrophobic substances (Casparian Strip) to restrict apoplastic flow of water to the inside.Coles PhillipsSymmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Generalizability theory: Generalizability theory, or G Theory, is a statistical framework for conceptualizing, investigating, and designing reliable observations. It is used to determine the reliability (i.Canna Leaf Roller: Cannas are largely free of pests, but in the USA plants sometimes fall victim the Canna Leaf Roller, which can actually be two different insects. Larva of the Brazilian skipper butterfly (Calpodes ethlius), also known as the Larger Canna Leaf Roller, cut the leaves and roll them over to live inside while pupating and eating the leaf.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Dark matter halo: A dark matter halo is a hypothetical component of a galaxy that envelops the galactic disc and extends well beyond the edge of the visible galaxy. The halo's mass dominates the total mass.YjdF RNA motifMetabolome: The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism.MicroRNA and microRNA target database: This microRNA database and microRNA targets databases is a compilation of databases and web portals and servers used for microRNAs and their targets. MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (ncRNAs) that regulate gene expression by targeting messenger RNAs.Pituitary-specific positive transcription factor 1: POU domain, class 1, transcription factor 1 (Pit1, growth hormone factor 1), also known as POU1F1, is a transcription factor for growth hormone.Flower box: __NOTOC__Phacidiopycnis padwickii: Phacidiopycnis padwickii is a plant pathogen infecting chickpea.Microsatellite: A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 2–5 base pairs) are repeated, typically 5-50 times. Microsatellites occur at thousands of locations in the human genome and they are notable for their high mutation rate and high diversity in the population.Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.Chromosome regionsMac OS X Server 1.0Nif regulonMasayori Inouye: Masayori Inouye is a Japanese biochemist who, along with his team, discovered natural antisense RNA.RV coefficient: In statistics, the RV coefficientWeedy rice: Weedy rice, also known as red rice, is a variety of rice (Oryza) that produces far fewer grains per plant than cultivated rice and is therefore considered a pest. The name "weedy rice" is used for all types and variations of rice which show some characteristic features of cultivated rice and grow as weeds in commercial rice fields.Open reading frame: In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA).Fungicide use in the United States: A more accurate title for this page would be "Common plant pathogens to food crops in the United States".Alternative splicing: Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.WGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.FasX small RNA: In molecular biology, the FasX small RNA (fibronectin/fibrinogen-binding/haemolytic-activity/streptokinase-regulator-X) is a non-coding small RNA (sRNA) produced by all group A Streptococcus. FasX has also been found in species of group D and group G Streptococcus.Breeding for drought stress tolerancePhenotype microarray: The phenotype microarray approach is a technology for high-throughput phenotyping of cells.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Gossypium herbaceum: Gossypium herbaceum, commonly known as Levant cotton, is a species of cotton native to the semi-arid regions of sub-Saharan Africa and Arabia where it still grows in the wild as a perennial shrub. It is a sister-species of Gossypium arboreum.Proteomics Standards Initiative: The Proteomics Standards Initiative (PSI) is a working group of Human Proteome Organization. It aims to define data standards for proteomics in order to facilitate data comparison, exchange and verification.Soil salinity control: Soil salinity control relates to controlling the problem of soil salinity and reclaiming salinized agricultural land.Global microbial identifier: The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.Silverleaf whiteflyCS-BLASTTransfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Maladaptation: A maladaptation () is a trait that is (or has become) more harmful than helpful, in contrast with an adaptation, which is more helpful than harmful. All organisms, from bacteria to humans, display maladaptive and adaptive traits.Boletus auriflammeus: Boletus auriflammeus, commonly known as the flaming gold bolete, is a species of bolete fungus in the family Boletaceae. Described as new to science in 1872, it is found in eastern North America, where it grows in a mycorrhizal association with oaks.Kandel (mountain): The Kandel is a mountain, 1,241.4 metres high, in the Black Forest in the south of Baden-Württemberg, Germany.Populus tremula: Populus tremula, commonly called aspen, common aspen, Eurasian aspen, European aspen, or quaking aspen, is a species of poplar native to cool temperate regions of Europe and Asia, from Iceland and the British IslesJames Kilkelly Irish native Aspen tree east to Kamchatka, north to inside the Arctic Circle in Scandinavia and northern Russia, and south to central Spain, Turkey, the Tian Shan, North Korea, and northern Japan. It also occurs at one site in northwest Africa in Algeria.

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

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)

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

 (+info)

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

 (+info)

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

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)

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

 (+info)

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

 (+info)

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

 (+info)

(8/4463) 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.

 (+info)



cDNA


  • In single-cell transcriptome studies, it is critical to obtain high-quality cDNA libraries from individual cells that represent the original in vivo mRNAs as closely as possible. (clontech.com)

Sequencing


  • This webinar will describe a protocol and proof-of-principle experiments for Cellular Indexing of Transcriptome and Epitopes by Sequencing (CITE-seq). (genomeweb.com)
  • Ozsolak F., Milos P.M. (2011) Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing. (springer.com)

Analysis


  • Is the Subject Area "Transcriptome analysis" applicable to this article? (plos.org)

Methods


  • Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools for understanding cellular physiology and human disease biology, and have begun to be utilized in various clinical diagnostic applications. (springer.com)

Cells


  • The core SMART technology in this kit is an immensely powerful tool for studying the full transcriptome, including splice junctions and alternative splicing events in cells, and provides full-length gene coverage. (clontech.com)

quantities


  • The efficacy of amplification of small quantities of total RNA with the TransPlex ® Complete Whole Transcriptome Amplification Kit ( WTA2 ) was examined in this study. (sigmaaldrich.com)
  • This study confirms that the TransPlex Complete Whole Transcriptome Amplification Kit can effectively amplify low input quantities of RNA, approaching the single cell level. (sigmaaldrich.com)

studies


  • RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. (hindawi.com)

levels


  • According to this view, RNA was considered a "bridge" in the transfer of biological information between DNA and proteins, whereas the identity of each expressed gene, and of its transcriptional levels, were commonly indicated as "transcriptome" [ 2 ]. (hindawi.com)