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Series GSE34557 Query DataSets for GSE34557
Status Public on Jun 24, 2012
Title Diverse epigenetic strategies interact to control epidermal differentiation [Illumina bead array]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary It is becoming clear that interconnected functional gene networks, rather than single genes in isolation, govern stem cell self-renewal and differentiation. To identify potential epigenetic networks that impact on human epidermal stem cells we performed siRNA based genetic screens for 332 chromatin modifiers. We developed a Bayesian mixture model to predict putative functional interactions between those epigenetic modifiers that regulated differentiation. This allowed us to discover a network of genetic interactions involving EZH2, UHRF1 (both known to regulate epidermal self-renewal), ING5 (a MORF complex component), BPTF and SMARCA5 (NURF complex components). Genome-wide localisation and global mRNA expression analysis revealed that these factors impact two distinct but functionally related gene sets, including integrin extracellular matrix receptors that mediate anchorage of epidermal stem cells to their niche. Using a competitive epidermal reconstitution assay we confirmed that ING5, BPTF, SMARCA5, EZH2 and UHRF1 control differentiation under physiological conditions. Thus, regulation of distinct gene expression programs through the interplay between diverse epigenetic strategies protects epidermal stem cells from differentiation.
 
Overall design Primary human keratinocytes (line Lka, passage 2) were cultured in Keratinocyte Serum Free Medium (KSFM) to 70% confluency in 10 cm dishes. Cells were treated with: vehicle (0.2% DMSO), the EGFR inhibitor AG1478 (10 uM), recombinant human BMP2/7 heterodimer (200 ng/ml) or a combination of AG1478+BMP2/7 (10 uM and 200 ng/ml, respectively) for 48 hours. RNA was extracted directly using a Qiagen RNeasy kit
 
Contributor(s) Mulder KW, Watt FM
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Submission date Dec 19, 2011
Last update date Feb 18, 2019
Contact name Chandra Chilamakuri
E-mail(s) datasubmissions@cruk.cam.ac.uk
Organization name Cancer Research UK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (1)
GPL6884 Illumina HumanWG-6 v3.0 expression beadchip
Samples (12)
GSM851007 C9 P2_vehicle A
GSM851008 H9 P2_AG1478 C
GSM851009 C10 P2_AG1478 BMP2.7 C
This SubSeries is part of SuperSeries:
GSE34558 Diverse epigenetic strategies interact to control epidermal differentiation
Relations
BioProject PRJNA156423

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
GSE34557_RAW.tar 6.3 Mb (http)(custom) TAR
GSE34557_non-normalized.txt.gz 4.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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