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Status |
Public on Dec 03, 2013 |
Title |
donor1_CD34+_d0 |
Sample type |
genomic |
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|
Source name |
Hematopoietic stem and progenitor cells from umbilical cord blood
|
Organism |
Homo sapiens |
Characteristics |
donor: donor1 cell type: CD34+ fraction passage: freshly isolated
|
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
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|
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.
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|
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Submission date |
Sep 12, 2012 |
Last update date |
Dec 03, 2013 |
Contact name |
Wolfgang Wagner |
E-mail(s) |
wwagner@ukaachen.de
|
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 |
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