GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
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
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
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
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap