CEL-Seq is a RNA sequencing technique designed to overcome the limitation of small starting amounts of RNA, often used for single-cell RNA sequencing.
In this protocol, samples are barcoded and pooled before linear amplification of mRNA via IVT.
During the sample preparation, each mRNA transcript is tagged with a Unique Molecular Identifier (UMI), which is used during the bioinformatics analysis to collapse reads originated from the same transcript.
In order to account for pipetting variation, spike-ins of a known concentration may be added to individual samples at the beginning of sample preparation. Data is then mapped and counted according to the known spike-in sequences and annotations. Using the expected counts of spike-ins, correlation plots and statistics are generated.