Abstract

High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method for overcoming this limitation by barcoding and pooling samples before linearly amplifying mRNA with the use of one round of in vitro transcription. We show that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method. We demonstrate the power of this method by studying early C. elegans embryonic development at single-cell resolution. Differential distribution of transcripts between sister cells is seen as early as the two-cell stage embryo, and zygotic expression in the somatic cell lineages is enriched for transcription factors. The robust transcriptome quantifications enabled by CEL-Seq will be useful for transcriptomic analyses of complex tissues containing populations of diverse cell types.

Keywords

BiologyTranscriptomeComputational biologyRNA-SeqGeneRNAZygoteSomatic cellGene expressionTranscription (linguistics)Single-cell analysisCellPoolingCell biologyGeneticsEmbryogenesisComputer science

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Year
2012
Type
article
Volume
2
Issue
3
Pages
666-673
Citations
1258
Access
Closed

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Cite This

Tamar Hashimshony, Florian Wagner, Noa Sher et al. (2012). CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. Cell Reports , 2 (3) , 666-673. https://doi.org/10.1016/j.celrep.2012.08.003

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DOI
10.1016/j.celrep.2012.08.003