|
| Status |
Public on Aug 28, 2010 |
| Title |
TEL-AML1 ChIP 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
TEL-AML1 ChIP DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: REH
chip antibody: anti-TEL (Santa Cruz Biotechnology)
|
| Treatment protocol |
ChIP antibody to TEL (Santa Cruz Biotechnology) was used.
|
| Growth protocol |
The B-cell precursor leukemic cell line REH was grown in 24-well plates (Nunc, Roskilde, Denmark) at 106 cells/mL and was cultured in 6-well plates in RPMI with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested, and chromatin was formalin crosslinked and sheared to approximately 200–1000 bp using a Sonic Dismembrator model 550 at settings 1.5, for 2–4 cycles 50 s per cycle on ice. The chromatin DNA complexes were then isolated following the microarray application protocol as described in the kit (EZ-ChIP Kit).
|
| Label |
Cy5
|
| Label protocol |
At least 4 ug of ligation-mediated PCR-amplified DNA was used to carry out the labeling step.
|
| |
|
| Channel 2 |
| Source name |
Input DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: REH
chip antibody: none
|
| Treatment protocol |
The chromatin DNA that was not immunoprecipitated served as the input DNA
|
| Growth protocol |
The B-cell precursor leukemic cell line REH was grown in 24-well plates (Nunc, Roskilde, Denmark) at 106 cells/mL and was cultured in 6-well plates in RPMI with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested, and chromatin was formalin crosslinked and sheared to approximately 200–1000 bp using a Sonic Dismembrator model 550 at settings 1.5, for 2–4 cycles 50 s per cycle on ice. The chromatin DNA complexes were then isolated following the microarray application protocol as described in the kit (EZ-ChIP Kit).
|
| Label |
Cy3
|
| Label protocol |
At least 4 ug of ligation-mediated PCR-amplified DNA was used to carry out the labeling step.
|
| |
|
| |
| Hybridization protocol |
Hybridization was carried out according to Nimblegen's standard protocol
|
| Scan protocol |
Tiling Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
|
| Description |
TEL-AML1 ChIP chip, microRNA promoter arrays
|
| Data processing |
ChIP-chip data were normalized using the scatter plot smoother lowess based on all probes. For analysis of significant “enrichment,” data were first sorted according to genomic locations, and a window of size of 500bp moving along the genome was adopted, centering at each probe. For each probe, the median log-ratio of neighbor probes residing in the window was calculated; typically with 10 probes within each window.
|
| |
|
| Submission date |
Aug 27, 2010 |
| Last update date |
Aug 27, 2010 |
| Contact name |
Joseph Leo Wiemels |
| E-mail(s) |
[email protected]
|
| Phone |
415 514-0577
|
| Fax |
415 502-7411
|
| Organization name |
UCSF
|
| Lab |
Epidemiology
|
| Street address |
1450 3rd Street, MC 0520
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL10861 |
| Series (1) |
| GSE23842 |
TEL-AML1 regulation of survivin and apoptosis via miRNA-494 and miRNA-320a |
|
