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Set of all RNA molecules in one cell or a population of cells
The transcriptome is the set of all RNA molecules (transcripts) in a cell or a population of cells. It includes all of the functional RNA molecules and
Transcriptome
Transcriptome instability is a genome-wide, pre-mRNA splicing-related characteristic of certain cancers. In general, pre-mRNA splicing is dysregulated
Transcriptome_instability
Study of RNA transcripts
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an
Transcriptomics_technologies
Lab technique in cellular biology
biological sample, providing a snapshot of the transcriptome at a specific time. It enables transcriptome-wide analysis by sequencing cDNA derived from
RNA-Seq
Digital transcriptome subtraction (DTS) is a bioinformatics method to detect the presence of novel pathogen transcripts through computational removal
Digital transcriptome subtraction
Digital_transcriptome_subtraction
Analysis technique of genes
Single-cell transcriptomics refers to the quantification and analysis of the transcriptomes of individual cells. Single-cell transcriptomics makes it possible to
Single-cell_transcriptomics
De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome. As a result of
De novo transcriptome assembly
De_novo_transcriptome_assembly
Transcriptome-wide association study (TWAS) is a genetic methodology that can be used to compare the genetic components of gene expression and the genetic
Transcriptome-wide association study
Transcriptome-wide_association_study
American genetics researcher
genomes, transcriptomes, proteomes, and other high-throughput omics datasets. His lab has contributed to understanding the genomes and transcriptomes of yeast
Michael_P._Snyder
Full-Parasites is a transcriptome database of apicomplexa parasites. apicomplexa Tuda, Josef; Mongan Arthur E; Tolba Mohammed E M; Imada Mihoko; Yamagishi
Full-parasites
Tumors research program
and the transcriptome. Precision medicine Oncology Cancer Research Bioinformatics Computational genomics Oncogenomics Genomics Transcriptome Gene expression
CIT Program Tumor Identity Cards
CIT_Program_Tumor_Identity_Cards
Sequences remaining within RNA after RNA splicing
the transcriptome, which is all of the transcribed RNA within a cell type. While the exome is constant from cell-type to cell-type, the transcriptome changes
Exome
Order of flowering plants
placement of the Myrtales in the Malvid clade by the One Thousand Plant Transcriptomes Initiative. Myrtales are placed as a sister to the eurosids II clade
Myrtales
Measure of the completeness of DNA sequencing
sequencing machine, allowing coverages of >108. Deep sequencing of transcriptomes, also known as RNA-Seq, provides both the sequence and frequency of
Coverage_(genetics)
The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a database of alternatively spliced human transcripts based on H-Invitational. Alternative
Human-transcriptome DataBase for Alternative Splicing
Human-transcriptome_DataBase_for_Alternative_Splicing
Former international research effort
The 1000 Plant Transcriptomes Initiative (1KP) was an international research effort to establish the most detailed catalogue of genetic variation in plants
1000_Plant_Genomes_Project
Software in bioinformatics
most commonly used in bioinformatic studies to assemble genomes or transcriptomes. Two common types of de novo assemblers are greedy algorithm assemblers
De_novo_sequence_assemblers
Study of the structure of plants
conservation and diversification of plant morphologies. In these studies, transcriptome conservation patterns were found to mark crucial ontogenetic transitions
Plant_morphology
Computational methods in biology
processes. Single-cell omics technologies have extended beyond the transcriptome to profile diverse physical and chemical properties at single-cell resolution
Single-cell multi-omics integration
Single-cell_multi-omics_integration
RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
but whose local functions are largely unknown. Tiling arrays aid in transcriptome mapping as well as in discovering sites of DNA/protein interaction (ChIP-chip
Tiling_array
Discipline in genetics
Roychowdhury S, Chinnaiyan AM (2016). "Translating cancer genomes and transcriptomes for precision oncology". CA. 66 (1): 75–88. doi:10.3322/caac.21329.
Genomics
UniGene was a NCBI database of the transcriptome and thus, despite the name, not primarily a database for genes. Each entry is a set of transcripts that
UniGene
Species of legume
valuable red "rosewood" timber. University of Oxford published the transcriptomes of Dalbergia oliveri and five other Dalbergia spp. It was found that
Dalbergia_oliveri
Set of proteins that can be expressed by a genome, cell, tissue, or organism
Bioinformatics List of omics topics in biology Plant Proteome Database Transcriptome Interactome Human Proteome Project BioPlex Human Protein Atlas Johnson
Proteome
Division of plant life
distantly related red algal hosts. As enlisted in realDB, 27 complete transcriptomes and 10 complete genomes sequences of red algae are available. Listed
Red_algae
Species of flowering plant
Yang, Chaowei; Zhou, Haijiang; Qiao, Jie (2021). "Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia"
Paulownia_catalpifolia
American bioengineer and molecular biologist
for Biological Studies, where he developed CRISPR-Cas13 systems for transcriptome engineering. In 2020, he joined the bioengineering faculty at the University
Patrick_Hsu
Species of snake
expressed genes. Out of these genes, 12,346 belonged to the venom gland transcriptome, which included 139 genes from 33 toxin gene families. Additionally
Indian_cobra
Reduction of blood flow to the heart
Coronary artery disease (CAD), also called coronary heart disease (CHD), or ischemic heart disease (IHD), is a type of heart disease involving the reduction
Coronary_artery_disease
RNA sequencing of isolated and/or microdissected cell nuclei
into cDNA after emulsion breakage. Sequencing this cDNA produces the transcriptomes of all the single nuclei being looked at and these can be used for many
SnRNA-seq
Superphylum of bilateral animals
Xenacoelomorpha and could form the Xenambulacraria group, but recent transcriptome analyses concluded that the phylum Xenacoelomorpha is the sister group
Deuterostome
Complete set of small molecules in a biological sample
of proteins (the proteome) and the complete set of transcripts (the transcriptome). The first book on metabolomics was published in 2003. The first journal
Metabolome
Swiss-American bioengineer and neuroscientist
S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD (April 2018). "Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors". Cell. doi:10
Silvana_Konermann
DNA sequencing method
strands. It can also be used for whole-genome and region sequencing, transcriptome analysis, metagenomics, small RNA discovery, methylation profiling,
Illumina_dye_sequencing
Process by which a gene can code for multiple proteins
technology, researchers were able to update the human adenovirus type 2 transcriptome and document the presence of 904 splice variants produced by the virus
Alternative_splicing
Chemical and systems biology researcher
developed CRISPR-Genome Organization (CRISPR-GO) based on dCas9 and CRISPR-Transcriptome Organization (CRISPR-TO) based on dCas13. Qi is a co-inventor of the
Lei_Stanley_Qi
5′ end of the messenger RNA population in a biological sample (the transcriptome). The small fragments (historically 27 nucleotides long, but now limited
Cap analysis of gene expression
Cap_analysis_of_gene_expression
diverse populations, including people with genetic disorders or cancers Transcriptome analysis is the study of all the RNA transcripts that are produced by
Linked-read_sequencing
Suborder of bats
Koopman to refer to certain families of microbats). Recent studies using transcriptome data have found strong support for the Yinpterochiroptera–Yangochiroptera
Yinpterochiroptera
Hybrid between a sheep and a goat
parent–species combination has an influence on hybrid fertility. Blood transcriptome analysis of a buck–ewe hybrid and its parents revealed significant deviations
Sheep–goat_hybrid
American biotechnology company
D.; Hut, Roelof A.; Panda, Satchidananda (2024-09-03). "Multi-organ transcriptome atlas of a mouse model of relative energy deficiency in sport". Cell
Seer,_Inc.
Laboratory technique
inhibitors. The addition of RNase inhibitors, such as EGTA, enhances transcriptome analysis by preserving higher quality RNA from the samples. Recording
Patch-sequencing
Type of DNA library
into a collection of host cells, which constitute some portion of the transcriptome of the organism and are stored as a "library." cDNA is produced from
CDNA_library
Family of beetles
Seidel, Matthias; Eberle, Jonas; Misof, Bernhard; et al. (2023). "A transcriptome-based phylogeny of Scarabaeoidea confirms the sister group relationship
Scarabaeidae
Species of legume
and forest landscape restoration. University of Oxford published the transcriptomes of Dalbergia cochinchinensis and five other Dalbergia spp. It was found
Dalbergia_cochinchinensis
Order of insects that includes grasshoppers
monophyletic. A recent comprehensive phylogeny based on analyses of data from transcriptomes and mitochondrial genomes found the following relationships within Orthoptera
Orthoptera
Cultivar of kiwifruit
pre-harvest bagging treatment on kiwifruit appearance and quality via transcriptome and metabolome analyses". Food Research International. 173 (Pt 1) 113276
Red_kiwifruit
Nucleic acid motif in molecular biology
site in most transcripts of archaeal and eukaryotic mRNA. Archaeal transcriptomes use a mix of Kozak sequence, leaderless initiation and, more rarely
Kozak_consensus_sequence
Species of single-celled organism
as an example of a protozoan and also as an example of symbiosis. A transcriptome sequence is determined. Moreover, a combination of long-read sequencing
Paramecium_bursaria
Type of endocrine gland cancer
Bidkhori G, et al. (August 2017). "A pathology atlas of the human cancer transcriptome". Science. 357 (6352) eaan2507. Bibcode:2017Sci...357n2507U. doi:10
Pancreatic_cancer
Examines sequence information from individual cells
This platform of single-cell RNA sequencing allows the analysis of transcriptomes on a cell-by-cell basis by the use of microfluidic partitioning to capture
Single-cell_sequencing
Molecule for mRNA-capture
A transcriptome in vivo analysis tag (TIVA tag) is a multifunctional, photoactivatable mRNA-capture molecule designed for isolating mRNA from a single
Transcriptome in vivo analysis tag
Transcriptome_in_vivo_analysis_tag
Species of fish
G.; Duong, Thuy-Yen; Wang, Xu; Dunham, Rex A. (2021). "Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus
Iridescent_shark
All of the contents of a cell including organelles but excluding the nucleus
and from the nucleus. The study found that CMX compartmentalizes the transcriptome, proteome, and metabolome, and that CMX-associated ribosomes exhibit
Cytoplasm
Species of butterfly
adaptation and speciation in tiger swallowtail butterflies using de novo transcriptome assemblies". Genome Biology and Evolution. 5 (6): 1233–1245. doi:10
Papilio_appalachiensis
Biological analysis approach
the genome, epigenome, transcriptome, proteome, metabolome, exposome, and microbiome (i.e., a meta-genome or meta-transcriptome, depending upon how it
Multiomics
Suborder of annelids
a Tree: A Robust Phylogeny for Terebelliformia (Annelida) Based on Transcriptomes, Molecular and Morphological Data". Biology. 9 (4): 73. doi:10.3390/biology9040073
Terebelliformia
Lobster or crab organs eaten as a delicacy
the Crab Portunus trituberculatus: Gene Discovery in the Comparative Transcriptome of Different Hepatopancreas Stages Effects of estradiol on fatty acid
Tomalley
Common name for many species of fish
Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis". Animals. 11 (12): 3538. Bibcode:2021Anima..11.3538C. doi:10
Tilapia
Species of moth
at the tensan silk genes in more detail a de novo genome and set of transcriptomes have been sequenced, producing a 700Mb reference with 15,481 genes.
Antheraea_yamamai
Rose family of flowering plants
recently Xiang et al. (2017) recovered these relationships using nuclear transcriptomes: Rosoideae has been identified as the earliest branching subfamily by
Rosaceae
Clade of eukaryotes containing land plants and some algae
Proterozoic. In 2019, a phylogeny of the Archaeplastida based on genomes and transcriptomes from 1,153 plant species was proposed. The placing of algal groups is
Archaeplastida
Species group of the subgenus Drosophila
subgenus Drosophila. A number of species have had their genomes or transcriptomes sequenced for evolutionary studies using Drosophila. The following species
Immigrans-tripunctata radiation
Immigrans-tripunctata_radiation
Species of plant
(June 2019). "De novo sequencing analysis of the Rosa roxburghii fruit transcriptome reveals putative ascorbate biosynthetic genes and EST-SSR markers".
Rosa_roxburghii
Species of annelid worm
spines; applying isopropanol to the area may help alleviate the pain. The transcriptome of the bearded fireworm was sequenced and annotated in 2015. de Kluijver
Hermodice_carunculata
Cellular biology lab technique
CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) is a method for performing RNA sequencing along with gaining quantitative and
CITE-Seq
will mean these barriers no longer hold true. Any organism's entire transcriptome could be potentially sequenced in one run (for very small bacterial
SOLiD_sequencing
Subspecies of insect
latest date for the adoption of clothing by humans. However, recent transcriptome analyses casts doubt on whether lice provide a means to date the origin
Body_louse
American homeopathic company
Traumeel appeared to have a broad ‘phytocellular’ effect on the wound transcriptome by altering the balance of cell types present in the wound. "MediNatura
Heel_(corporation)
Estimation of embryo quality for in vitro fertilization
can vary in extent from a single target biomarker to entire genomes, transcriptomes, proteomes and metabolomes. The results may be used to score embryos
Embryo_quality
Class of parthenogenetic freshwater rotifers
phylogenomic analysis of syndermatan relationships" to date was based on transcriptome data from all four groups, and provided "strong support" for the hypothesis
Bdelloidea
Genus of deciduous conifers
The genus Cathaya was included in some older studies, but based on transcriptome analysis, is now considered closer to Pinus and Picea. The split of
Larch
Species group of the subgenus Drosophila
Mushroom-feeding Drosophila (mycophagous Drosophila) are a subset of Drosophila flies that have highly specific mushroom-breeding ecologies. Often these
Mushroom-feeding_Drosophila
Species of archaeon
carboxydotrophic pathway and bears seven different hydrogenase complexes. The transcriptome analysis of this organism has also been done. It has been found that
Thermococcus_barophilus
Species of cricket
Brenda; Perkin, Lindsey C.; Lorenzen, Marcé D.; Dossey, Aaron T. (2020). "Transcriptome analysis of life stages of the house cricket, Acheta domesticus, to
House_cricket
End of an organism's life
circulatory system. Masamoto Y, Piraino S, Miglietta MP (December 2019). "Transcriptome Characterization of Reverse Development in Turritopsis dohrnii (Hydrozoa
Death
Cancer of the colon or rectum
Lee S, et al. (August 2017). "A pathology atlas of the human cancer transcriptome". Science. 357 (6352) eaan2507. Bibcode:2017Sci...357n2507U. doi:10
Colorectal_cancer
Subtype of serotonin receptor
determined through combinatorial genome-wide association study and transcriptome analysis". Animal Genetics. 51 (5): 741–751. doi:10.1111/age.12980.
5-HT2A_receptor
Venom-producing mammals
"Understanding and utilising mammalian venom via a platypus venom transcriptome". Journal of Proteomics. 72 (2): 155–164. doi:10.1016/j.jprot.2008.12
Venomous_mammal
Sub-sequence DNA in genetics
species). EST approaches have largely been superseded by whole genome and transcriptome sequencing and metagenome sequencing. An EST results from one-shot sequencing
Expressed_sequence_tag
Species of bacteria
Single-cell transcriptomics using single-cell RNA-Seq gave the complete transcriptome of H. pylori which was published in 2010. This analysis of its transcription
Helicobacter_pylori
Cell line derived from human embryonic kidney cells
comprehensive study of the genomes and transcriptomes of HEK 293 and five derivative cell lines compared the HEK 293 transcriptome with that of human kidney, adrenal
HEK_293_cells
Edible annual grass native to Ethiopia and Eritrea
Journal of Botany, 87, 9–17. Cannarozzi, G.; et al. (2014). "Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis
Teff
sequencing is not limited to WG sequencing and can also include exome, transcriptome, micronome sequencing, and end-sequence profiling. These methods can
Cancer_genome_sequencing
Private crewed spaceflight to the International Space Station in 2025
(Indian Institute of Science) — Survival, revival, reproduction, and transcriptome of the eutardigrade Paramacrobiotus sp. BLR strain in space. Voyager
Axiom_Mission_4
Species of reptile
biology (ev-devo). A 2019 study assembled an annotated, multi-tissue transcriptome for the veiled chameleon to use as a resource in evolutionary and developmental
Veiled_chameleon
Clade of plants with xylem and phloem
Dickerman, Allan W.; Beers, Eric P. (June 2005). "The Xylem and Phloem Transcriptomes from Secondary Tissues of the Arabidopsis Root-Hypocotyl". Plant Physiology
Vascular_plant
Laboratory technique to multiply a DNA sample for study
primers (probes) to amplify DNA sequences from a sequenced genome or transcriptome. In silico PCR was proposed as an educational tool for molecular biology
Polymerase_chain_reaction
DNA section marked with start and stop codon of different length
for data containing multiple smaller FASTA sequences, such as de-novo transcriptome assemblies. Coding region Putative gene Sequerome – A sequence profiling
Open_reading_frame
Species of mite
weather warms up. Recently, researchers at USDA-ARS published the whole transcriptome of WCM, and showed that WSMV infection alters gene expression of its
Aceria_tosichella
Clade of archaeplastids including green algae and the land plants
Embryophyta (land plants) In 2019, a phylogeny based on genomes and transcriptomes from 1,153 plant species was proposed. The placing of algal groups is
Viridiplantae
Species of small, biologically immortal jellyfish
Masaki; Ohara, Osamu; Kubota, Shin (2016-08-01). "De Novo Assembly of the Transcriptome of Turritopsis, a Jellyfish that Repeatedly Rejuvenates". Zoological
Turritopsis_dohrnii
Genus of worms
volucris Mendoza-Franco, Violante-González & Vidal-Martínez, 2008 The transcriptome of Rhabdosynochus viridisi has been studied in 2022, and G-Protein-Coupled-Receptors
Rhabdosynochus
Burning tobacco and inhaling the smoke
tobacco consumption is rising by 3.4% per year. Smoking alters the transcriptome of the lung parenchyma; the expression levels of a panel of seven genes
Tobacco_smoking
Subspecies of flowering plant
"Candidate chemosensory genes identified in Colaphellus bowringi by antennal transcriptome analysis". BMC Genomics. 16 1028. doi:10.1186/s12864-015-2236-3. PMC 4667470
Napa_cabbage
Open access DNA sequence database
submission types, including whole genome shotgun (WGS) assemblies, transcriptome shotgun assemblies (TSA), targeted locus studies (TLS), and high-throughput
GenBank
Phylum of animals
phylum was considered to be a member of the deuterostomes, but later transcriptome analyses have suggested that the phylum Xenacoelomorpha is a sister
Xenacoelomorpha
Species of Gram-positive bacterium
competence genes: mapping of the SigH, ComK1 and ComK2 regulons by transcriptome sequencing". Molecular Microbiology. 94 (3): 557–579. doi:10.1111/mmi
Staphylococcus_aureus
Species of annelid worm
evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species". Scientific Reports. 7 (1)
Eulagisca_gigantea
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