CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

TLDR

High‑throughput sequencing enables detailed gene‑expression profiling, but single‑cell analysis is limited by the tiny amounts of RNA available. The authors aim to apply CEL‑Seq to study early Caenorhabditis elegans embryogenesis at single‑cell resolution. CEL‑Seq barcodes and pools samples, then linearly amplifies mRNA with a single round of in‑vitro transcription, allowing sensitive, reproducible quantification. CEL‑Seq outperforms PCR‑based amplification, detects differential transcript distribution between sister cells as early as the two‑cell stage, shows transcription‑factor enrichment in somatic lineages, and provides robust data useful for dissecting complex tissues.

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.