|
| Status |
Public on Oct 31, 2013 |
| Title |
MCF7_MBD3_Rep1 [GPL10671] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MBD3-Dam bound DNA from MCF-7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
replicate: 1
fraction: MBD3-Dam bound DNA
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Cells were cultured with DMEM/F12 supplemented with 10% fetal bovine serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified and processed for DamID as described in Nature Protocol 2007;2(6):1467-78.
|
| Label |
cy5
|
| Label protocol |
1ug DNA was labeled with Nimblegen Dual-Color DNA labeling kit followed by NimbleGen Arrays User's Guide (version 6.2)
|
| |
|
| Channel 2 |
| Source name |
Dam bound DNA from MCF-7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
replicate: 1
fraction: Dam bound DNA
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Cells were cultured with DMEM/F12 supplemented with 10% fetal bovine serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified and processed for DamID as described in Nature Protocol 2007;2(6):1467-78.
|
| Label |
Cy3
|
| Label protocol |
1ug DNA was labeled with Nimblegen Dual-Color DNA labeling kit followed by NimbleGen Arrays User's Guide (version 6.2)
|
| |
|
| |
| Hybridization protocol |
Hybridizaion was performed followed by NimbleGen Arrays User's Guide (version 6.2)
|
| Scan protocol |
Scanning was performed as described in Lai AY et al. (J Exp Med. 2010 Aug 30;207(9):1939-50)
|
| Data processing |
The log2(Cy5) values were normalized using loess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. The normalized values presented here are the residuals obtained from loess regression (log2(cy5) was treated as dependent and log2(cy3) as explanatory variables) for CG count bin. These approach is similar to localized MA loess normalization the difference being that instead of predicting M (log2(Cy5/cy3)) using A (log2(cy5*cy3)) locally (using subset of probes) we attempt to predict log2(cy5) using log2(cy3) using probes that are similar in terms of their CG count. The multiple signal values from same probe within array were averaged. Furthermore, the resulting signal values for MIRA and ChIP-antibody samples were quantile normalized independently to adjust for between sample variations.
|
| |
|
| Submission date |
Mar 01, 2013 |
| Last update date |
Nov 02, 2013 |
| Contact name |
Deepak Mav |
| Organization name |
Sciome LLC
|
| Street address |
2 Davis Drive
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL10671 |
| Series (2) |
| GSE44773 |
DamID for MBD3 in human breast cancer cell lines [Promoter_Arrays] |
| GSE44776 |
DamID for MBD3 in human breast cancer cell lines |
|
