|
| Status |
Public on Jul 19, 2007 |
| Title |
Jurkat-NRSF-mAb_Human Tiling 2.0R G Array |
| Sample type |
genomic |
| |
|
| Source name |
Jurkat - T cell leukaemia derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for NRSF/REST using two different antibodies in Jurkat cells
|
| Treatment protocol |
The background model was created using reverse crosslinked chromatin, instead of a ChIP, which was amplified and hybed to arrays with the same protocol as the ChIP samples. Two different antibodies were used: a custom mAb (Mortazavi et al., 2006) and a polyclonal Ab from Upstate (catalog 07-579).
|
| Growth protocol |
We used a several growths of Jurkat cells to produce chromatin according to standard procedures (after Johnson et al., 2007). 4x10^7 cells were used for each chromatin IP.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin extracted according to standard procedures (after Johnson et al., 2007).
|
| Label |
biotin
|
| Label protocol |
Each individual ChIP was amplified using a random primer amplification protocol (Cooper et al., 2007), except 2mM dUTP was added to the 10mM dNTP mix. Four ChIPs were pooled for each replicate array set. Two positive QPCR primers were used to QC each pool of IPs. Labeling thereafter was according to standard Affymetrix protocols.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to manufacturer's instructions.
|
| Scan protocol |
According to standard Affymetrix protocols.
|
| Description |
chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for NRSF/REST using two different antibodies in Jurkat cells
|
| Data processing |
We used MAT (Johnson et al., 2006) to process the raw CEL files. The following settings were used: BandWidth = 300, MaxGap = 300, MinProbe = 10, Trim = 0.1, pvalue=1e-5.
|
| |
|
| Submission date |
Jul 16, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
David Scott Johnson |
| E-mail(s) |
seasquirtdoctor@gmail.com
|
| Phone |
650-725-3018
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Richard M. Myers
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL4916 |
| Series (1) |
| GSE8489 |
ChIP-chip analysis of transcription factors GABP, SRF, TAF, and NRSF on Affymetrix whole genome tiling arrays 2.0R |
|
