Validation of noise models for single-cell transcriptomics

被引：0

作者：

Grun, Dominic ^{[1
,2
]}

Kester, Lennart ^{[1
,2
]}

van Oudenaarden, Alexander ^{[1
,2
]}

机构：

[1] Royal Netherlands Acad Arts & Sci, Hubrecht Inst KNAW, Utrecht, Netherlands

[2] Univ Med Ctr Utrecht, Canc Genom Netherlands, Utrecht, Netherlands

来源：

NATURE METHODS | 2014年 / 11卷 / 06期

基金：

欧洲研究理事会;

关键词：

MESSENGER-RNA-SEQ; EXPRESSION; MOLECULES;

D O I：

10.1038/NMETH.2930

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Single-cell transcriptomics has recently emerged as a powerful technology to explore gene expression heterogeneity among single cells. Here we identify two major sources of technical variability: sampling noise and global cell-to-cell variation in sequencing efficiency. We propose noise models to correct for this, which we validate using single-molecule FISH. We demonstrate that gene expression variability in mouse embryonic stem cells depends on the culture condition.

引用

页码：637 / +

页数：7

共 25 条

[1]

Anders S., 2010, GENOME BIOL, V11, pR106, DOI [10.1186/gb-2010-11-10-r106, DOI 10.1186/gb-2010-11-10-r106]

[2] The external RNA controls consortium: a progress report [J].

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 .

NATURE METHODS, 2005, 2 (10) :731-734

[3]

Brennecke P, 2013, NAT METHODS, V10, P1093, DOI [10.1038/NMETH.2645, 10.1038/nmeth.2645]

[4] A LIMITED MEMORY ALGORITHM FOR BOUND CONSTRAINED OPTIMIZATION [J].

BYRD, RH ;

LU, PH ;

NOCEDAL, J ;

ZHU, CY .

SIAM JOURNAL ON SCIENTIFIC COMPUTING, 1995, 16 (05) :1190-1208

[5] Functional roles for noise in genetic circuits [J].

Eldar, Avigdor ;

Elowitz, Michael B. .

NATURE, 2010, 467 (7312) :167-173

[6] CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification [J].

Hashimshony, Tamar ;

Wagner, Florian ;

Sher, Noa ;

Yanai, Itai .

CELL REPORTS, 2012, 2 (03) :666-673

[7] Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation [J].

Hug, H ;

Schuler, R .

JOURNAL OF THEORETICAL BIOLOGY, 2003, 221 (04) :615-624

[8]

Islam S, 2014, NAT METHODS, V11, P163, DOI [10.1038/NMETH.2772, 10.1038/nmeth.2772]

[9] Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq [J].

Islam, Saiful ;

Kjallquist, Una ;

Moliner, Annalena ;

Zajac, Pawel ;

Fan, Jian-Bing ;

Lonnerberg, Peter ;

Linnarsson, Sten .

GENOME RESEARCH, 2011, 21 (07) :1160-1167

[10] Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types [J].

Jaitin, Diego Adhemar ;

Kenigsberg, Ephraim ;

Keren-Shaul, Hadas ;

Elefant, Naama ;

Paul, Franziska ;

Zaretsky, Irina ;

Mildner, Alexander ;

Cohen, Nadav ;

Jung, Steffen ;

Tanay, Amos ;

Amit, Ido .

SCIENCE, 2014, 343 (6172) :776-779

← 1 2 3 →