Cell Expression by Linear Amplification Sequencing

CEL-Seq uses barcoding and pooling of RNA to overcome challenges from low input (Hashimshony et al., 2012). In this method, each cell undergoes RT with a unique barcoded primer in its individual tube. After second-strand synthesis, cDNAs from all reaction tubes are pooled and PCR-amplified. Paired-end deep sequencing of the PCR products allows for accurate detection of sequence information derived from both strands.

Similar methods: CEL-Seq2, Quartz-Seq, Drop-seq, MARS-Seq, CytoSeq, inDrop, Hi-SCL


  • Barcoding and pooling allow for multiplexing and studying many different single cells at a time
  • Cross-contamination is greatly reduced due to using 1 tube per cell
  • Fewer steps than single-cell tagged reverse-transcription sequencing (STRT-Seq)
  • Very little read-length bias (Bhargava et al., 2014)
  • Strand-specific


  • Strongly 3′ biased (Shapiro et al., 2013)
  • Abundant transcripts are amplified preferentially
  • Requires at least 400 pg of total RNA


Illumina Library prep and Array Kit Selector


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