CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.
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.
Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
Tamar
T
Hashimshony
Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
Naftalie
N
Senderovich
Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
Gal
G
Avital
Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
Agnes
A
Klochendler
Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
Yaron
Y
de Leeuw
Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
Leon
L
Anavy
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.|Department of Biology, MIT, Cambridge, MA, 02139, USA.|Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA.
Dave
D
Gennert
Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA, 94080, USA.
Shuqiang
S
Li
Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA, 94080, USA.
Kenneth J
KJ
Livak
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.|Department of Biology, MIT, Cambridge, MA, 02139, USA.|Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA.
Orit
O
Rozenblatt-Rosen
Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
Yuval
Y
Dor
Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.|Department of Biology, MIT, Cambridge, MA, 02139, USA.|Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA.
Aviv
A
Regev
Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel. yanai@technion.ac.il.
Itai
I
Yanai
D000465:Algorithms; D000818:Animals; D002453:Cell Cycle; D002478:Cells, Cultured; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*