|
| Status |
Public on Jul 15, 2015 |
| Title |
RNApolII-E2-siNCAPG_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
beast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
chip antibody: RNApolII
antibody vendor/catalog#: SC-899, Santa Cruz Biotech
treatment: cells transfected with siNCAPG, and 1hr with 100nM E2, crosslinked with 1% formaldehyde
|
| Treatment protocol |
Before experiment, the cells were changed to deficient MEM plus 5% charcoal treated phenol red free medium to culture for 3 days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 1hr.
|
| Growth protocol |
MCF7 obtained from ATCC were cultured in α-MEM media supplemented with 10% FBS in a 5% CO2 humidified incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were crosslinked with 1% of formaldehyde or double-crosslinked with DSG first followed by 1% of formaldehyde, clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors of Truseq system from Illumina, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
cells transfected with siNCAPG, and 1hr treatment with 100nM E2, crosslinked with 1% formaldehyde, RNA PolII ChIPseq was then performed.
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
|
| |
|
| Submission date |
Oct 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Qi Ma |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSD
|
| Street address |
9500 Gilman Dr,
|
| City |
San Diego |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE62222 |
Interphase condensins regulate ligand-depedent enhancer activation (ChIP-seq) |
| GSE62229 |
Interphase condensins regulate ligand-depedent enhancer activation |
|
| Relations |
| BioSample |
SAMN03103621 |
| SRA |
SRX730449 |
