|
| Status |
Public on Jan 29, 2018 |
| Title |
BJ_ATAC_R1 |
| Sample type |
SRA |
| |
|
| Source name |
ATACseq Pre-FOXA2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: BJ-5ta
cell type: immortalized BJ foreskin fibroblast cell line
genotype/variation: FOXA2 doxycycline inducible cell line
treated with: none (uninduced)
|
| Treatment protocol |
To induce FOXA2, doxycycline was added at .5ug/mL.
Cells were halted in G1 by the addition of 200uM Mimosine (Sigma) treatment over night. To induce FOXA2, doxycycline was added at .5ug/mL.
|
| Growth protocol |
Clonal FOXA2 doxycycline inducible cells lines were derived from an immortalized BJ foreskin fibroblast cell line from ATCC (BJ-5ta; CRL-4001). Cells were cultured in MEM-Alpha (Life technologies: 32561-037) with 10% FBS, 1% pen-strep, .01mg/mL hygromycin B and 5ng/mL bFGF. Derived BJFOXA2 lines were grown in the same conditions plus .5ug/mL Puromycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tagmentation was performed on whole nuclei at 37C for 45 minutes as previously described in (Buenrostro et al., 2013). DNA was isolated on PCR min-elute columns (Qiagen) and a small amount of the DNA was amplified for 9, 12 and 15 cycles to determine optimal cycling conditions.
Nextera amplified
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing read were aligned to human genome (hg19) using bowtie with default parameters
Peaks for TF ChIPs were called using MACS2 and IDR framework.
IDR called FOXA2 peaks from several tissues were further processed using in-house pipeline. Peaks from different cells were merged together if they were found to be overlapping. New peak summit for these merged peak was calcualted based on their relative contributions (heights) as a measure of distance. After calculating and assigning new peak summit to the merged peaks, peaks boundries were also redefined by extending them by 300 bps in both directions from the newly assigned peak summit.
These peaks were then used for downstream analysis. We calculated RPKM for these 600bp peaks. A meta table was created for these 600bp peaks with RPKM values for all TFs, histone marks as well as ATAC signal
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with coordinates and RPKM.
|
| |
|
| Submission date |
Nov 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sudhir Thakurela |
| Organization name |
HSCRB
|
| Street address |
7 Divinity Avenue
|
| City |
Cambridge |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE90453 |
Genetic determinants and epigenetic effects of pioneer factor binding [ATAC-seq] |
| GSE90456 |
Genetic determinants and epigenetic effects of pioneer factor binding |
|
| Relations |
| BioSample |
SAMN06049695 |
| SRA |
SRX2368874 |
