|
| Status |
Public on Mar 09, 2018 |
| Title |
IMR90 Etop Input |
| Sample type |
SRA |
| |
|
| Source name |
Fetal lung fibroblasts IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
cell type: Human fetal lung fibroblasts
treatment agent: DMSO
chip antibody: none
|
| Treatment protocol |
Samples were treated with either vehicle or indicated doses of etoposide for indicated amout of time before extraction of DNA.
|
| Growth protocol |
Cells were grown in DMEM supplemented with 10%FBS
Cells were passaged in 10cm corningware dishes using media described in Samples section in a 37°C humidified incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from sub-confluent dishes, fixed and sheared to an average length of 200-1500bp. 10% of the samples from each cell line were pooled to form the Input. RNAPII/BRCA1 antibody was used for immunoprecipitation. ChIP DNA was purified, sheared further to an average length of 350 bp and sequenced after library construction.
Sequencing library was prepared using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Short reads were aligned to hg19 using BWA with default alignment parameters, and then post processed to limit to unique alignment and no more than 2 mis-match base-pairs
Peak calling by using MACS2 with parameters as follows: -g 2.7e9 -q 0.05 -B -m 3 30, and using corresponding Input as control sample
peaks (in bed file format) were further annotated to gene by using CEAS (v1.0.2)
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bed format, which are the peak calling results by using MACS2.
|
| |
|
| Submission date |
Sep 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yidong Chen |
| E-mail(s) |
[email protected]
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE68847 |
BRCA1, R-loops and Recombination defects in Ewing's sarcoma |
| GSE87324 |
BRCA1/RNApII regulation in Ewing's sarcoma (ChIP-seq) |
|
| Relations |
| BioSample |
SAMN05821215 |
| SRA |
SRX2188687 |
