GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE38557

Query DataSets for GSE38557

Status

Public on Jul 15, 2012

Title

DNA methylation dynamics during in vivo differentiation of blood and skin stem cells

Organism

Mus musculus

Experiment type

Expression profiling by array
Third-party reanalysis

Summary

DNA methylation is a mechanism of epigenetic regulation that is common to all vertebrates. Functional studies support its relevance for tissue homeostasis, but the global dynamics of DNA methylation during in vivo differentiation have not been worked out in detail. Here we report high-resolution DNA methylation maps of adult stem cell differentiation in mouse, focusing on 19 purified cell populations of the blood and skin lineages. Except for global demethylation in erythrocytes, observed DNA methylation changes were locus-specific and relatively modest in size. They frequently overlapped with lineage-associated transcription factors and their binding sites, suggesting that DNA methylation may protect cells from aberrant transcription factor activation. DNA methylation and gene expression provided highly complementary information, and combining the two enabled us to infer the blood lineage hierarchy directly from genomic data. In summary, our dataset and analysis demonstrate that in vivo differentiation of adult stem cells is associated with small but informative changes in the distribution of DNA methylation across the mouse genome.

Overall design

We used microarray data to compare the gene expression profiles between various purified cell populations of the blood and skin lineages. Microarray data were obtained for 13 blood cell types (HSC, MPP1, MPP2, CLP, CMP, MEP, GMP, CD4, CD8, B-cell, Eryth, Granu, Mono) and 6 skin cell types (TBSC, ABSC, MTAC, CLDC, EPro, EDif). A subset of these microarray profiles have already been uploaded to GEO as part of previous research and were reused for the current study (GSE20244: MPP1, MPP2, CLP, CMP, GMP; GSE6506: CD4, CD8, B-cell, Eryth, Granu, Mono; GSE31028: TBSC, ABSC, MTAC). All microarray profiles that had not been made public previously are included here (HSC, MEP, CLDC, EPro, EDif). Furthermore, all data are available for download from the paper's supplementary website (http://invivomethylation.computational-epigenetics.org/).

This submission includes the gene expression component of the study.

The complete dataset representing the GSE38557 Samples, and the GSE20244, GSE6506, and GSE31028 Samples listed above, is linked below as a supplementary file.

Contributor(s)

Bock C, Beerman I, Lien WH, Rossi DJ, Meissner A

Citation(s)

22841485

Submission date

Jun 07, 2012

Last update date

Feb 11, 2019

Contact name

Christoph Bock

E-mail(s)

cbock@cemm.oeaw.ac.at

Organization name

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

Street address

Lazarettgasse 14

City

Vienna

ZIP/Postal code

1090

Country

Austria

Platforms (1)

GPL1261

[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array

Samples (10)

More...

GSM945546	Hematopoietic stem cell, biological replicate 1
GSM945547	Hematopoietic stem cell, biological replicate 2
GSM945548	Megakaryocyte-erythroid progenitor, biological replicate 1

Relations

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE38557_RAW.tar	33.6 Mb	(http)(custom)	TAR (of CEL)
GSE38557_complete_dataset.txt.gz	5.8 Mb	(ftp)(http)	TXT
Processed data included within Sample table
Processed data are available on Series record