Cel-seq2

Each cell-specific barcode labels the cDNA generated from one cell, so material can later be pooled while its cellular origin remains recoverable. A unique molecular identifier adds a label at the transcript level, supporting more quantitative interpretation of detected molecules. Together, these sequence features let CEL-Seq2 separate cellular expression profiles from a shared library rather than treating the sample as one averaged population.

The T7 promoter supplies a common entry point for in vitro transcription after cDNA from cells has been pooled. This transcription step provides linear amplification, increasing the amount of material available for library construction while retaining the barcode-based organization needed to assign expression measurements to their originating cells. Its role therefore connects pooled processing with cell-resolved transcriptome analysis.

Because CEL-Seq2 uses oligo(dT) primers, reverse transcription is directed toward polyadenylated RNA. The resulting measurements therefore represent the polyadenylated transcript population captured by this primer strategy, rather than an undifferentiated inventory of every RNA species. This feature is central to interpreting the assay’s gene-expression profiles and comparing transcript abundance among individual cells within a heterogeneous sample.

Pooling cDNA after cell-specific labeling allows material from many cells to be processed together while expression values remain attributable to individual cells. That retained identity enables researchers to examine variation among cells, recognize distinct cell types or developmental states, and detect disease-associated or condition-dependent transcriptional changes that could be obscured in a population-wide average.

A CEL-Seq2 workflow begins with barcoded oligo(dT)-primed reverse transcription of RNA from individual cells. The resulting cDNA carries the cell barcode, unique molecular identifier, and sequence information associated with captured transcripts. cDNA is then pooled, subjected to in vitro transcription through the T7 promoter for linear amplification, and used to generate sequencing libraries. This order preserves cell assignment through shared processing.

Researchers can apply CEL-Seq2 when a biological sample contains multiple cellular populations or states and the goal is to resolve their transcriptional differences. Supported use cases include identifying cell types, examining developmental states, assessing disease-associated changes, and measuring responses to experimental conditions. The output connects gene-expression patterns with individual-cell heterogeneity, providing context that an aggregate profile would not provide.