{"entity":{"id":"bulk-rna-seq","kind":"term","name":"Bulk RNA sequencing (RNA-seq) and the full transcriptome","aka":["bulk RNA-seq","bulk RNA sequencing","bulk transcriptome","bulk expression","full transcriptome","whole transcriptome","transcriptome-wide expression","~20k genes"],"tldr":"Bulk RNA sequencing reads all the messenger RNA in a piece of tumour at once, giving one averaged expression value per gene for the whole sample.","summary":"RNA-Seq is a next-generation sequencing technique that quantifies and identifies the RNA molecules in a sample, a snapshot of the transcriptome at one time, by sequencing cDNA made from RNA (Wikipedia). Bulk means the whole tissue is processed together, so the profile averages cancer, stromal and immune cells. The transcriptome is the set of all RNA transcripts; the roughly twenty thousand protein-coding genes are the full-transcriptome feature set that gene panels subsample.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/RNA-Seq","links":[{"label":"Wikipedia: transcriptome","url":"https://en.wikipedia.org/wiki/Transcriptome"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/RNA-Seq"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":["rna-seq"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["tpm-fpkm-counts","star-salmon","single-cell-rna-seq","tumour-purity"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/bulk-rna-seq."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Genomics & genetics"},"route":"/terms/bulk-rna-seq/","neighbours":{"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"microarray-expression","kind":"term","name":"Microarray expression data","route":"/terms/microarray-expression/"},{"id":"single-cell-rna-seq","kind":"term","name":"Single-cell RNA sequencing (scRNA-seq, 10x Chromium)","route":"/terms/single-cell-rna-seq/"},{"id":"star-salmon","kind":"term","name":"STAR and Salmon (RNA-seq alignment and quantification)","route":"/terms/star-salmon/"},{"id":"tpm-fpkm-counts","kind":"term","name":"TPM, FPKM and raw counts (expression units)","route":"/terms/tpm-fpkm-counts/"},{"id":"tumour-purity","kind":"term","name":"Tumour purity","route":"/terms/tumour-purity/"}],"technology":[{"id":"rna-seq","kind":"technology","name":"RNA sequencing & expression profiling","route":"/technologies/rna-seq/"}]}}