|
| Status |
Public on Jul 01, 2013 |
| Title |
GR ChIP-Seq Afos (+E2) r1 |
| Sample type |
SRA |
| |
|
| Source name |
7438 cells + Afos
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse mammary cells (express GFP-GR, Cherry-ER, and Afos under a tet regulated promoter)
treatment: Estradiol for 30 minutes
cell line: 7438 cells
replicate: replicate 1
chip antibodies: cocktail of PA-510A and PA-511A from Affinity BioReagents and sc-1004 from Santa Cruz
|
| Treatment protocol |
Cells were plated for experiments in DMEM growth medium supplemented with 10% charcoal-dextran serum with tetracyline 48 hours prior to conducting the experiment. Twenty-four hours before hormone treatment, cells were washed three times with phosphate-buffered saline and fresh DMEM with 10% charcoal-dextran serum (no tetracyline) was added to the cells to induce expression of GFP-GR and Ch-ER. Cells were untreated or induced with 100nM dexamethasone, 100nM estradiol, or 100nM dexamethasone plus 100nM estradiol for 30 mins.
|
| Growth protocol |
For maintenance cells were cultured in DMEM supplemented with 10% calf serum, sodium pyruvate, non-essential amino acids, and 5 ug/ml tetracycline to repress expression of the tet-regulated fusion proteins.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and GR-DNA complexes or ER-DNA complexes were isolated with antibody
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
GR-ChIP in cells treated with E2 - replicate 1
|
| Data processing |
Illumina Casava 1.8 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%. Peaks with the maximum tag density lower than 10 were eliminated.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: comma-delimited (CSV) text files include genomic locations (Chromosome, start, end ), z-score, p-value and the maximum density of hotspots.
|
| |
|
| Submission date |
Apr 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Songjoon Baek |
| Organization name |
NCI / NIH
|
| Department |
CCR
|
| Lab |
LRBGE
|
| Street address |
41 Library Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE46123 |
ER and GR crosstalk at the Genomic Level in mouse mammary cells |
| GSE46124 |
ER, GR, and E2 |
|
| Relations |
| BioSample |
SAMN02046692 |
| SRA |
SRX268259 |
