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 transcriptional program


Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

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All measurements, including biological measurements, contain a tradeoff between precision and throughput. In sequencing-based measurements like mRNA-sequencing (mRNA-seq), precision is determined largely by the sequencing depth applied to individual samples. At high sequencing depth, mRNA-seq can detect subtle changes in gene expression including the expression of rare splice variants or quantitative modulations in transcript abundance. However, such precision comes at a cost, and sequencing transcripts from 10,000 single cells at deep sequencing coverage (106 reads per cell) currently requires 2 weeks of sequencing on an Illumina HiSeq 4000. Not all biological questions require such extreme technical sensitivity. For example, a catalog of human cell types and the transcriptional programs that define them can potentially be generated by querying the general transcriptional state of single cells ( Trapnell, 2015 Defining cell types and states with single-cell genomics.