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Series GSE52529 Query DataSets for GSE52529
Status Public on Mar 23, 2014
Title Pseudo-temporal ordering of individual cells reveals regulators of differentiation
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Single-cell expression profiling by RNA-Seq promises to exploit cell-to-cell variation in gene expression to reveal regulatory circuitry governing cell differentiation and other biological processes. Here, we describe Monocle, a novel unsupervised algorithm for ordering cells by progress through differentiation that dramatically increases temporal resolution of expression measurements. This reordering unmasks switch-like changes in expression of key regulatory factors, reveals sequentially organized waves of gene regulation, and exposes regulators of cell differentiation. A functional screen confirms that a number of these regulators dramatically alter the efficiency of myoblast differentiation, demonstrating that single-cell expression analysis with Monocle can uncover new regulators even in well-studied systems.
 
Overall design We selected primary human myoblasts as a model system of cell differentiation to investigate whether ordering cells by progress revealed new regulators of the process. We sequenced RNA-Seq libraries from each of several hundred cells taken over a time-course of serum-induced differentiation.
Please note that this dataset is a single-cell RNA-Seq data set, and each cell comes from a capture plate. Thus, each well of the plate was scored and flagged with several QC criteria prior to library construction, which are provided as sample characteristics; CONTROL indicates that this library is a off-chip tube control library constructed from RNA of approximately 250 cells and 'DEBRIS' indicates that the well contained visible debris (and may or may not include a cell). Libraries marked DEBRIS thus cannot be confirmed to come from a single cell.
 
Contributor(s) Trapnell C, Cacchiarelli D, Grimbsby J, Pokharel P, Li S, Morse M, Mikkelsen T, Rinn J
Citation(s) 24658644
Submission date Nov 19, 2013
Last update date May 15, 2019
Contact name Cole Trapnell
E-mail(s) cole@broadinstitute.org
Organization name Harvard University
Department Stem Cell and Regenerative Biology
Lab John Rinn
Street address 7 Divinity Ave
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (384)
GSM1268960 Cell T0_CT_A01
GSM1268961 Cell T0_CT_A02
GSM1268962 Cell T0_CT_A03
Relations
BioProject PRJNA229164
SRA SRP033135

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52529_fpkm_matrix.txt.gz 10.9 Mb (ftp)(http) TXT
GSE52529_truseq_fpkm_matrix.txt.gz 1.1 Mb (ftp)(http) TXT
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Processed data are available on Series record
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