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Sample GSM1001928 Query DataSets for GSM1001928
Status Public on Dec 03, 2013
Title donor2_CD34-_d7_TCP
Sample type genomic
Source name Hematopoietic stem and progenitor cells from umbilical cord blood
Organism Homo sapiens
Characteristics donor: donor2
cell type: CD34- fraction
passage: 7d on TCP
Treatment protocol CD34+ cells were isolated from fresh umbilical cord blood after written consent according to the guidelines specifically approved by the Ethic Committee of RWTH Aachen University (Permit Number: EK187/08) using the CD34 Micro Bead Kit on a MiniMACS system (Miltenyi Biotec GmbH, Bergisch-Gladbach, Germany). Cells were cultured in StemSpan serum free expansion medium (Stem Cell Technologies, Grenoble, France) supplemented with 10 µg/mL heparin (ratiopharm, GmbH, Ulm, Germany), 20 ng/mL thrombopoietin (TPO; PeproTech GmbH, Hamburg, Germany), 10 ng/mL stem cell factor (SCF; PeproTech), 10 ng/mL fibroblast growth factor 1 (FGF1; PeproTech). Culture was either performed on tissue culture plastic (TCP) or on a confluent layer of mesenchymal stromal cells (MSCs; passage 3 to 6). After seven days, CD34+ and CD34- fractions were again separated as described above.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from 10(6) cells using the Qiagen DNA Blood Midi Kit.
Label Cy5 and Cy3
Label protocol Standard Infinium HD Methylation Assay protocol
Hybridization protocol Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.
Scan protocol Standard Infinium HD Methylation Assay protocol
Data processing Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.
Submission date Sep 12, 2012
Last update date Dec 03, 2013
Contact name Wolfgang Wagner
Phone +49 241 8088611
Organization name RWTH Aachen University
Department Helmholtz Institute for Biomedical Engineering
Lab Stem Cell Biology and Cellular Engineering
Street address Pauwelsstrasse 20
City Aachen
ZIP/Postal code 52074
Country Germany
Platform ID GPL13534
Series (2)
GSE40799 DNA methylation profiles of freshly isolated CD34+ cells and upon expansion on either tissue culture plastic (TCP) or mesenchymal stromal cells (MSCs)
GSE40800 In vitro Expansion of Hematopoietic Stem and Progenitor Cells Induces Tightly Regulated DNA-Hypermethylation

Data table header descriptions
VALUE Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.74234 0
cg00000108 0.9400165 0
cg00000109 0.8795095 0
cg00000165 0.1734496 0
cg00000236 0.8539409 0
cg00000289 0.7491223 0
cg00000292 0.8619234 0
cg00000321 0.3083598 0
cg00000363 0.3616116 0
cg00000622 0.0182818 0
cg00000658 0.812667 0
cg00000714 0.4029234 0
cg00000721 0.9182289 0
cg00000734 0.09037504 0
cg00000769 0.07752328 0
cg00000807 0.8714664 0
cg00000884 0.8511274 0
cg00000905 0.08707611 0
cg00000924 0.5591012 0
cg00000948 0.9005942 0

Total number of rows: 485577

Table truncated, full table size 10981 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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