|
| Status |
Public on May 12, 2010 |
| Title |
ASCu Rep 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Adipose MSC ChIP DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mesenchymal stem cells
tissue: Adipose tissue
medip antibody: 5-methyl cytosine antibody, Diagenode
|
| Treatment protocol |
The mesenchymal stem cells were transfected with H3.3-EGFP and sorted by FACS 168 hrs post transfection.
|
| Growth protocol |
The mesenchymal stem cells were cultured for seven passages in DMEM/F12 containing 20% FCS and 1 % PenStrep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified and fragmented by sonication to 300-500 bp fragments. 5-methylcytosine (5-mC)-enriched fragments were immunoprecipitated using anti-5mC antibodies. Precipitated and input DNA was amplified using the WGA2 kit (Sigma-Aldrich) and cleaned up. Input and MeDIP DNA were labeled with Cy3 and Cy5 respectively and hybridized on promoter arrays.
|
| Label |
Cy5
|
| Label protocol |
Labeling done by Nimblegen as per normal service protocol
|
| |
|
| Channel 2 |
| Source name |
Input DNA from H3.3-EGFP transfected mesenchymal stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mesenchymal stem cells
tissue: Adipose tissue
chip antibody: none, input DNA
|
| Treatment protocol |
The mesenchymal stem cells were transfected with H3.3-EGFP and sorted by FACS 168 hrs post transfection.
|
| Growth protocol |
The mesenchymal stem cells were cultured for seven passages in DMEM/F12 containing 20% FCS and 1 % PenStrep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified and fragmented by sonication to 300-500 bp fragments. 5-methylcytosine (5-mC)-enriched fragments were immunoprecipitated using anti-5mC antibodies. Precipitated and input DNA was amplified using the WGA2 kit (Sigma-Aldrich) and cleaned up. Input and MeDIP DNA were labeled with Cy3 and Cy5 respectively and hybridized on promoter arrays.
|
| Label |
Cy3
|
| Label protocol |
Labeling done by Nimblegen as per normal service protocol
|
| |
|
| |
| Hybridization protocol |
Hybridization done by Nimblegen as per normal service protocol
|
| Scan protocol |
Scanning done by Nimblegen as per normal service protocol
|
| Description |
ASCu Rep 1
|
| Data processing |
log2 (ChIP/Input) with biweight mean of values subtracted
|
| |
|
| Submission date |
Sep 24, 2009 |
| Last update date |
May 12, 2010 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
|
| Department |
Institute of Basic Medical Sciences
|
| Street address |
PO Box 1112 Blindern
|
| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
| |
|
| Platform ID |
GPL7408 |
| Series (1) |
| GSE17053 |
Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging, ChIP-chip, and MeDIP-chip data |
|
