|
| Status |
Public on May 12, 2010 |
| Title |
MPCu, MeDIP, Rep 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MeDIP DNA, undifferentiated skeletal MPC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skeletal muscle
cell type: mesenchymal stem cells
differentiation: undifferentiated
medip antibody: 5-methyl cytosine antibody
|
| Treatment protocol |
Genomic DNA was isolated, fragmented and used for MeDIP.
|
| Growth protocol |
The muscle progenitors were cultured in Lonza commercial medium for up to 4-8 passages.
|
| 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 (Diagenode). Precipitated and input DNA was amplified using the WGA2 kit (Sigma-Aldrich) and cleaned up.
|
| Label |
Cy5
|
| Label protocol |
Labeling done by NimbleGen as per normal service protocol. Input and MeDIP DNA were labeled with Cy3 and Cy5, respectively.
|
| |
|
| Channel 2 |
| Source name |
Input DNA, undifferentiated skeletal MPC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skeletal muscle
cell type: mesenchymal stem cells
differentiation: undifferentiated
medip antibody: none
|
| Treatment protocol |
Genomic DNA was isolated, fragmented, labeled and hybridized onto arrays.
|
| Growth protocol |
The muscle progenitors were cultured in Lonza commerciall medium for up to 4-8 passages
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified and fragmented by sonication to 300-500 bp fragments. Precipitated and input DNA was amplified using the WGA2 kit (Sigma-Aldrich) and cleaned up.
|
| Label |
Cy3
|
| Label protocol |
Labeling done by NimbleGen as per normal service protocol. Input and MeDIP DNA were labeled with Cy3 and Cy5, respectively.
|
| |
|
| |
| Hybridization protocol |
Hybridization done by NimbleGen as per normal service protocol. Labeled DNA was hybridized on promoter arrays.
|
| Scan protocol |
Scanning done by NimbleGen as per normal service protocol.
|
| Description |
MPCu_2_MeDIP
|
| Data processing |
log2 (MeDIP/Input) with biweight mean of values subtracted.
|
| |
|
| Submission date |
Jan 07, 2010 |
| 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 (2) |
| GSE19794 |
DNA methylation in progenitor cells: MeDIP study |
| GSE19795 |
DNA methylation in progenitor cells |
|
