|
| Status |
Public on Oct 01, 2009 |
| Title |
HaloCHIP CREB (no Forskolin) biological rep 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Hela Cells transfected with the HaloTag-CREB fusion constructs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa cells
genome/variation: HaloTag-CREB fusion construct
|
| Treatment protocol |
Cells were crosslinked with 0.75% formaldehyde for 10min at 22C.
|
| Growth protocol |
HeLa cells (2-4 x 105) were plated in a single well of a standard 6-well plate. After reaching 70-80% confluency, typically 18-24 hours later, cells were transfected with the HaloTag-CREB fusion constructs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed as described in http://www.usbweb.com/proto/78460a.pdf. HaloCHIP experiments were performed as described in http://www.promega.com/tbs/tm075/tm075.pdf.
|
| Label |
Cy5
|
| Label protocol |
Standard Nimblegen protocol
|
| |
|
| Channel 2 |
| Source name |
Hela Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa cells
|
| Treatment protocol |
Cells were crosslinked with 0.75% formaldehyde for 10min at 22C.
|
| Growth protocol |
HeLa cells (2-4 x 105) were plated in a single well of a standard 6-well plate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed as described in http://www.usbweb.com/proto/78460a.pdf. HaloCHIP experiments were performed as described in http://www.promega.com/tbs/tm075/tm075.pdf.
|
| Label |
Cy3
|
| Label protocol |
Standard Nimblegen protocol
|
| |
|
| |
| Hybridization protocol |
Standard Nimblegen protocol
|
| Scan protocol |
Standard Nimblegen protocol
|
| Description |
no additional information
|
| Data processing |
The raw data from the arrays were analyzed as follows: the log2 ratio (enriched-cy5/total input-cy3) was calculated for each probe and data were then smoothed by averaging across a sliding window of 3 neighbouring probes shifting 1 probe at a time, minimizing noise from single probes. The median and standard deviation were calculated from the smoothed ratios for each sample. The median was subtracted from each ratio and divided by the standard deviation to center and normalize the data from each array. To summarize the enrichment for an entire promoter, the top 4 probe values were averaged for a given promoter region to approximate the 75th percentile value. The raw data, normalized data, and collapsed data for each array are available as supplemental at the following site: www.switchgeargenomics.com/creb_supp_data/.
|
| |
|
| Submission date |
Sep 30, 2009 |
| Last update date |
Sep 30, 2009 |
| Contact name |
Danette Hartzell |
| E-mail(s) |
[email protected]
|
| Organization name |
Promega
|
| Street address |
2800 Woods Hollow Road
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53711 |
| Country |
USA |
| |
|
| Platform ID |
GPL9325 |
| Series (1) |
| GSE18347 |
CREB ChIP-chip and HaloCHIP-chip experiments |
|
