E-GEOD-40799 - DNA methylation profiles of freshly isolated CD34+ cells and upon expansion on either tissue culture plastic (TCP) or mesenchymal stromal cells (MSCs)

Status
Released on 3 December 2013, last updated on 9 December 2013
Organism
Homo sapiens
Samples (12)
Array (1)
Protocols (6)
Description
Hematopoietic stem and progenitor cells (HPCs) can be maintained in vitro, but the vast majority of their progeny loses “stemness” during culture. In this study, we have analyzed DNA methylation (DNAm) profiles of freshly isolated CD34+ cells and upon expansion on either tissue culture plastic (TCP) or mesenchymal stromal cells (MSCs). DNAm profiles of expanded CD34+ versus CD34- subsets reflected hematopoietic differentiation, whereas culture on TCP or MSCs had little impact. Notably, all cultured HPCs - even those which remained CD34 positive - acquired significant DNA-hypermethylation, particularly in up-stream promoter regions, shore-regions of CpG islands, and binding sides for PU.1 and RUNX1. Our results point to a coordinated epigenetic process which needs to be controlled to enhance self-renewal of HPCs in vitro. 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Experiment type
methylation profiling by array 
Contacts
Wolfgang Wagner <wwagner@ukaachen.de>, Bernd Denecke, Carola I Weidner, Martin Zenke, Monika Wölfler, Qiong Lin, Thomas Walenda
Citation
Hematopoietic Stem and Progenitor Cells Acquire Distinct DNA-Hypermethylation During in vitro Culture. Weidner CI, Walenda T, Lin Q, W�lfler MM, Denecke B, Costa IG, Zenke M, Wagner W. , Europe PMC 24284763
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-40799.idf.txt
Sample and data relationshipE-GEOD-40799.sdrf.txt
Processed data (1)E-GEOD-40799.processed.1.zip
Array designA-GEOD-13534.adf.txt
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