|
Status |
Public on Jun 04, 2013 |
Title |
H3K27ac_ChIPSeq_E2 |
Sample type |
SRA |
|
|
Source name |
MCF7
|
Organism |
Homo sapiens |
Characteristics |
cell line: MCF7 cell antibody: H3k27ac chip vendor/catalog: Abcam, ab4729 treatment: 1hr treatment with 100nM E2
|
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 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 Genome Analyzer IIx |
|
|
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 |
Apr 05, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Qi Ma |
E-mail(s) |
q1ma@ucsd.edu
|
Organization name |
UCSD
|
Street address |
9500 Gilman Dr,
|
City |
San Diego |
ZIP/Postal code |
92093 |
Country |
USA |
|
|
Platform ID |
GPL10999 |
Series (1) |
GSE45822 |
Functional Importance of eRNAs for Estrogen-dependent Gene Transcriptional Activation |
|
Relations |
SRA |
SRX261275 |
BioSample |
SAMN01999642 |
Named Annotation |
GSM1115992_H3K27ac-MCF7-E2.bigWig |