GeneCore is the in-house genomics service centre at EMBL
Transcriptome sequencing (often called RNA-seq) measures RNA molecules in a sample to show which genes are active and at what levels. It enables quantitative comparisons between conditions (e.g., treated vs untreated) and can reveal changes in cellular state and biological pathways. Practical differences between studies typically come from sample preparation, library design (e.g., poly(A) selection vs ribosomal RNA depletion), sequencing depth, and data analysis, which mainly influence sensitivity and the level of detail that can be resolved.
Is a sequencing method that enriches for messenger RNA (mRNA), typically by selecting polyadenylated RNA (poly(A)+), which represents transcripts produced by active genes. By sequencing these transcripts, it provides a snapshot of gene expression, showing which genes are expressed and at what levels, and it can also reveal alternative transcript isoforms depending on the assay design.
Ribosomal RNA depleted RNA-seq is a sequencing method in which ribosomal RNA is removed so that the remaining RNA, including mRNA, long non-coding RNAs, and other transcripts, can be analyzed. This approach provides a broad view of the transcriptome, not only protein-coding genes.
Quant-seq (3′-end seq ) is an RNA-seq approach that sequences the 3′ ends of polyadenylated transcripts near the poly(A) tail for efficient and cost-effective gene expression quantification across many samples. It can also be used to study alternative polyadenylation, but generally provides less information on full-length isoforms than standard RNA-seq.
“Mapping and quantifying mammalian transcriptomes by RNA-Seq“
“Optimized design of antisense oligomers for targeted rRNA depletion“
“QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis“