title: CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.
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.
authors.affiliation: Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Tamar
authors.initials: T
authors.lastname: Hashimshony
authors.forename: Florian
authors.initials: F
authors.lastname: Wagner
authors.forename: Noa
authors.initials: N
authors.lastname: Sher
authors.forename: Itai
authors.initials: I
authors.lastname: Yanai
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans; D005786:Gene Expression Regulation / Q000502:physiology; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D018510:RNA, Helminth / Q000096:biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018510:RNA, Helminth; D012333:RNA, Messenger