|
| Status |
Public on Dec 13, 2007 |
| Title |
SRC_EtOH_Rep2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MCF7 cells, treated for 45 minutes with EtOH or 17beta-estradiol (E2)
|
| Organism |
Homo sapiens |
| Characteristics |
MCF-7 breast cancer cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA immunoprecipitated (IP DNA) with specific antibodies
|
| Label |
Cy5
|
| Label protocol |
Random priming labeling
|
| |
|
| Channel 2 |
| Source name |
MCF7 cells, treated for 45 minutes with EtOH or 17beta-estradiol (E2)
|
| Organism |
Homo sapiens |
| Characteristics |
MCF-7 breast cancer cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Input DNA
|
| Label |
Cy3
|
| Label protocol |
Random priming labeling
|
| |
|
| |
| Hybridization protocol |
Input and IP DNA co-hybridized to the genomic array described above for 18 hours at 42°C using a TECAN HS400 hybridization machine.
|
| Scan protocol |
GenePix 4000B scanner (Axon)
|
| Description |
NA
|
| Data processing |
After filtering out the spots flagged for bad quality, the signal ratio of IP-DNA over Input-DNA was log2 transformed and normalized based on a set of control genes, as described in the array design and in the supplemental materials.
The "Upper" and "Lower" .gpr files (linked below as Supplementary files) represent the two replicate regions on the same microarray slide. The exact details of the microarray design have been published and can be found here: http://mcb.asm.org/cgi/content/full/27/14/5090?view=long&pmid=17515612
|
| |
|
| Submission date |
Dec 03, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
W. Lee Kraus |
| E-mail(s) |
lee.kraus@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL6229 |
| Series (1) |
| GSE9253 |
Genomic analyses of TF binding, histone acetylation and gene expression reveal classes of E2-regulated promoters |
|
