CEL-Seq

CEL-Seq

CEL-Seq uses barcoding and pooling of RNA to overcome challenges from low input. 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

Pros:

• 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
• Strand-specific

Cons:

• Strongly 3' biased¹
• Abundant transcripts are amplified preferentially
• Requires at least 400 pg of total RNA

• CEL-Seq: Hashimshony T., Wagner F., Sher N. and Yanai I. (2012) CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep 2: 666-673
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