CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq

TLDR

Single‑cell transcriptomics requires a method that is sensitive, accurate, and reproducible. The authors introduce CEL‑Seq2, a modified CEL‑Seq method with threefold higher sensitivity, lower costs, and reduced hands‑on time. The method was implemented on Fluidigm's C1 system, enabling on‑chip barcoding of single cells and detection of cell‑cycle–associated gene expression changes in mouse fibroblasts, and was benchmarked against Smart‑Seq to show superior sensitivity. These enhancements render CEL‑Seq2 uniquely suitable for single‑cell RNA‑Seq, offering improved economics, resolution, and ease of use.

Abstract

Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. We also compare with Smart-Seq to demonstrate CEL-Seq2's increased sensitivity relative to other available methods. Collectively, the improvements make CEL-Seq2 uniquely suited to single-cell RNA-Seq analysis in terms of economics, resolution, and ease of use.