|
| Status |
Public on Aug 11, 2010 |
| Title |
IgG control CHIP in CaCo2 array B Rep 2 |
| Sample type |
genomic |
| |
|
| Source name |
IgG control CHIP in CaCo2 array B
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Caco-2 colon cancer cells, 1 day post confluent
|
| Growth protocol |
Cells were grown in 10% FBS DMEM and grown until 1 day post confluent on 15 cm plates
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% formaldehyde for 10 minutes at 37 degrees, then washed with cold PBS and scraped into PBS, and resuspended in ChIP lysis buffer and immunoprecipitated and processed as described by Carroll, et al, 2005, PMID: 16009131 and as described in our current work.
|
| Label |
biotin
|
| Label protocol |
labeling, hybridization, and scanning were done using manufacturer's instructions (Affymetrix)
|
| |
|
| Hybridization protocol |
labeling, hybridization, and scanning were done using manufacturer's instructions (Affymetrix)
|
| Scan protocol |
labeling, hybridization, and scanning were done using manufacturer's instructions (Affymetrix)
|
| Description |
2B_Igg-F2_Hs7B.CEL
|
| Data processing |
Model Based analysis of tiling arrays (MAT) was used to process the data as described previously: Johnson, et al, 2006, PMID: 16895995
.bar files were generated as the output of default MAT analysis and can be visualized using the publically available Affymetrix Ingtegrated Genome Browser
|
| |
|
| Submission date |
Jun 25, 2010 |
| Last update date |
Aug 11, 2010 |
| Contact name |
Michael P Verzi |
| Organization name |
Rutgers, the State University of New Jersey
|
| Department |
Genetics
|
| Lab |
Verzi
|
| Street address |
145 Bevier Road
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL4911 |
| Series (1) |
| GSE22572 |
TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions |
|
