RNA sequencing
Sign in to savethumb|419x419px|Summary of RNA-Seq. Within the organism, genes are transcribed and (in a eukaryote|eukaryotic organism) spliced to produce mature mRNA transcripts (red). The mRNA is extracted from the organism, fragmented and copied into stable ds-cDNA (blue). The ds-cDNA is sequenced using high-throughput, short-read sequencing methods. These sequences can then be aligned to a reference genome sequence to reconstruct which genome regions were being transcribed. This data can be used to annotate where expressed genes are, their relative expression levels, and any alternative splice variants.
Research
375,304 papers- RNA sequencing: advances, challenges and opportunities.Nature reviews. Genetics · 2011
- From bulk, single-cell to spatial RNA sequencing.International journal of oral science · 2021
- RNA Sequencing.Anesthesiology · 2020
- Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2.Journal of visualized experiments : JoVE · 2021
- Single-Cell RNA Sequencing Technology Landscape in 2023.Stem cells (Dayton, Ohio) · 2024
via PubMed
Article
27 sectionsContents
- History
- Methods
- Library preparation
- Complementary DNA sequencing (cDNA-Seq)
- Small RNA/non-coding RNA sequencing
- Direct RNA sequencing
- Single-molecule real-time RNA sequencing
- Single-cell RNA sequencing (scRNA-Seq)
- Experimental considerations
- Analysis
- Transcriptome assembly
- Gene expression quantification
- Spike-ins for absolute quantification and detection of genome-wide effects
- Differential expression
- Alternative splicing
- Coexpression networks
- Variant discovery
- RNA editing (post-transcriptional alterations)
- Fusion gene detection
- Copy number analyses
- Biomarker discovery
- Multiomics
- Other emerging analysis and applications
- See also
- References
- Further reading
- External links
thumb|419x419px|Summary of RNA-Seq. Within the organism, genes are transcribed and (in a eukaryote|eukaryotic organism) spliced to produce mature mRNA transcripts (red). The mRNA is extracted from the organism, fragmented and copied into stable ds-cDNA (blue). The ds-cDNA is sequenced using high-throughput, short-read sequencing methods. These sequences can then be aligned to a reference genome sequence to reconstruct which genome regions were being transcribed. This data can be used to annotate where expressed genes are, their relative expression levels, and any alternative splice variants.
RNA-Seq (short for RNA sequencing) is a next-generation sequencing (NGS) technique used to quantify and identify RNA molecules in a biological sample, providing a snapshot of the transcriptome at a specific time. It enables transcriptome-wide analysis by sequencing cDNA derived from RNA. Modern workflows often incorporate pseudoalignment tools (such as Kallisto and Salmon) and cloud-based processing pipelines, improving speed, scalability, and reproducibility.