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Everything about Transcriptome
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 all other transcripts that may arise by spurious transcription or transcription of non-functional regions such as pseudogenes or virus fragments. A major goal of modern molecular biology is to determine which transcripts are functional and which ones are junk RNA. Wikipedia →
🧭 Start here: a 6-step reading path
- Read the overview: TranscriptomeA 5-minute orientation
- Skim a recent paper: TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironmentInfluential work since 2022
- Pick up a classic book: RNA-seq data analysisThe most-reprinted book on the subject
- Read the landmark paper: Full-length transcriptome assembly from RNA-Seq data without a reference genomeCited 19,970 times
- Go sideways: Transcriptomics technologiesA closely related topic
- Go sideways: Functional genomicsA closely related topic
📖 Definitions
Noun The complete set of RNA molecules (transcripts) produced in a cell or a population of cells.
🏆 Landmark papers (most cited)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
mRNA-Seq whole-transcriptome analysis of a single cell
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
Simultaneous epitope and transcriptome measurement in single cells
An anatomically comprehensive atlas of the adult human brain transcriptome
A pathology atlas of the human cancer transcriptome
🆕 Influential since 2022
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment
Spatial epigenome–transcriptome co-profiling of mammalian tissues
Improved transcriptome assembly using a hybrid of long and short reads with StringTie
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment
📚 Books worth reading
RNA-seq data analysisEija Korpelainen · 2014
Role Of The Transcriptome In Breast Cancer PreventionJose Russo · 2012- 📕Microbial Metagenomics, Metatranscriptomics, and MetaproteomicsEd DeLong · 2013
Forest Genomics and BiotechnologyMatias Kirst, Rick Meilan · 2020
Ranked by number of editions on Open Library, a rough measure of how lasting a book is.
🔗 Related topics
- Transcriptomics technologies Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content…
- Functional genomics Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use…
- Serial analysis of gene expression Serial analysis of gene expression (SAGE) is a transcriptomic technique used by molecular biologists to produce a snapshot of the messenger RNA population…
- RNA-Seq RNA-Seq (short for RNA sequencing) is a next-generation sequencing (NGS) technique used to quantify and identify RNA molecules in a biological sample,…
- Metatranscriptomics Metatranscriptomics is the set of techniques used to study gene expression of microbes within natural environments, i.e., the metatranscriptome. While…
- Spatial transcriptomics Spatial transcriptomics, or spatially resolved transcriptomics, is a method that captures positional context of transcriptional activity within intact…
- Complementary DNA In genetics, complementary DNA (cDNA) is DNA that was reverse transcribed (via reverse transcriptase) from an RNA (e.g., messenger RNA or microRNA). cDNA…
- Cap analysis of gene expression Cap analysis of gene expression (CAGE) is a gene expression technique used in molecular biology to produce a snapshot of the 5′ end of the messenger RNA…