|
| Status |
Public on Dec 03, 2013 |
| Title |
donor3_CD34-_d7_TCP |
| Sample type |
genomic |
| |
|
| Source name |
Hematopoietic stem and progenitor cells from umbilical cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
donor: donor3
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 |
| 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 |
|
