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

被引：736

作者：

Hashimshony, Tamar ^{[1
]}

Senderovich, Naftalie ^{[1
]}

Avital, Gal ^{[1
]}

Klochendler, Agnes ^{[2
]}

de Leeuw, Yaron ^{[1
]}

Anavy, Leon ^{[1
]}

Gennert, Dave ^{[3
,4
,5
]}

Li, Shuqiang ^{[6
]}

Livak, Kenneth J. ^{[6
]}

Rozenblatt-Rosen, Orit ^{[3
,4
,5
]}

Dor, Yuval ^{[2
]}

Regev, Aviv ^{[3
,4
,5
]}

Yanai, Itai ^{[1
]}

机构：

[1] Technion Israel Inst Technol, Dept Biol, IL-32000 Haifa, Israel

[2] Hebrew Univ Jerusalem, Hadassah Med Sch, Inst Med Res Israel Canada, Dept Dev Biol & Canc Res, IL-91010 Jerusalem, Israel

[3] Broad Inst Harvard & MIT, Klarman Cell Observ, Cambridge, MA 02142 USA

[4] MIT, Dept Biol, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[5] MIT, Howard Hughes Med Inst, Dept Biol, Cambridge, MA 02140 USA

[6] Fluidigm Corp, 7000 Shoreline Court,Suite 100, San Francisco, CA 94080 USA

来源：

GENOME BIOLOGY | 2016年 / 17卷

基金：

以色列科学基金会; 欧洲研究理事会;

关键词：

TRANSCRIPTOMICS;

D O I：

10.1186/s13059-016-0938-8

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：7

共 19 条

[1] HTSeq-a Python']Python framework to work with high-throughput sequencing data
Anders, Simon
Pyl, Paul Theodor
Huber, Wolfgang
[J]. BIOINFORMATICS, 2015, 31 (02) : 166 - 169
[2] The external RNA controls consortium: a progress report
Baker, SC
Bauer, SR
Beyer, RP
Brenton, JD
Bromley, B
Burrill, J
Causton, H
Conley, MP
Elespuru, R
Fero, M
Foy, C
Fuscoe, J
Gao, XL
Gerhold, DL
Gilles, P
Goodsaid, F
Guo, X
Hackett, J
Hockett, RD
Ikonomi, P
Irizarry, RA
Kawasaki, ES
Kaysser-Kranich, T
Kerr, K
Kiser, G
Koch, WH
Lee, KY
Liu, CM
Liu, ZL
Lucas, A
Manohar, CF
Miyada, G
Modrusan, Z
Parkes, H
Puri, RK
Reid, L
Ryder, TB
Salit, M
Samaha, RR
Scherf, U
Sendera, TJ
Setterquist, RA
Shi, LM
Shippy, R
Soriano, JV
Wagar, EA
Warrington, JA
Williams, M
Wilmer, F
Wilson, M
[J]. NATURE METHODS, 2005, 2 (10) : 731 - 734
[3] Design and Analysis of Single-Cell Sequencing Experiments
Gruen, Dominic
van Oudenaarden, Alexander
[J]. CELL, 2015, 163 (04) : 799 - 810
[4] Grün D, 2014, NAT METHODS, V11, P637, DOI [10.1038/NMETH.2930, 10.1038/nmeth.2930]
[5] CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification
Hashimshony, Tamar
Wagner, Florian
Sher, Noa
Yanai, Itai
[J]. CELL REPORTS, 2012, 2 (03): : 666 - 673
[6] Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation
Hug, H
Schuler, R
[J]. JOURNAL OF THEORETICAL BIOLOGY, 2003, 221 (04) : 615 - 624
[7] Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
Islam, Saiful
Kjallquist, Una
Moliner, Annalena
Zajac, Pawel
Fan, Jian-Bing
Lonnerberg, Peter
Linnarsson, Sten
[J]. GENOME RESEARCH, 2011, 21 (07) : 1160 - 1167
[8] Jaitin D A., Science
[9] Kivioja T, 2012, NAT METHODS, V9, P72, DOI [10.1038/NMETH.1778, 10.1038/nmeth.1778]
[10] Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells
Klein, Allon M.
Mazutis, Linas
Akartuna, Ilke
Tallapragada, Naren
Veres, Adrian
Li, Victor
Peshkin, Leonid
Weitz, David A.
Kirschner, Marc W.
[J]. CELL, 2015, 161 (05) : 1187 - 1201

← 1 2 →