|
| Status |
Public on Jun 05, 2015 |
| Title |
PGR_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
endometrial stromal cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary cells
passages: 2-4
health status: healthy, proliferative phase
antibody: PGR
antibody catalog: H-190/sc-7208
|
| Treatment protocol |
10nM 17β-estradiol, 100nM medroxyprogesterone acetate, and 1mM cAMP OPTI-MEM I reduced serum media supplemented with 2% stripped fetal bovine serum and antibiotic and antimycotics
|
| Growth protocol |
DMEM F12, 10% fetal bovine serum, antibiotic-antimycotic, HEPES and NaHCO3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3 -ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-300 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on GA2 (GAII).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
50-nt sequence reads identified by the Sequencing Service (using Ilumina's Hi-seq)
reads mapped to the genome using the BWA algorithm with default settings
tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp
density of fragments, in 32-nt bins divided genome, defined in BAR files
peaks were defined using MACS at the default settings
Genome_build: GRCh37.p2-Primary Assembly
|
| |
|
| Submission date |
Jun 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Francesco J DeMayo |
| E-mail(s) |
[email protected]
|
| Phone |
713-798-6241
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Cellular Biology
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE69539 |
Progesterone receptor transcriptome and cistrome in decidualized human endometrial stromal cells [ChIP] |
| GSE94038 |
Progesterone receptor transcriptome and cistrome in decidualized human endometrial stromal cells |
|
| Relations |
| BioSample |
SAMN03761822 |
| SRA |
SRX1048945 |
