|
| Status |
Public on Feb 13, 2018 |
| Title |
FoxA1 ChIP-exo replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 cell ChIP-exo
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: FoxA1 (Abcam, ab23738, Lot GR2923512)
cell line: MCF-7
cell type: epithelial
|
| Treatment protocol |
Cells were incubated in phenol red-free, charcoal stripped FBS for 48 hours and then treated for 1 hour with 17 β-estradiol (E2, Sigma) at 100 μM.
Cells were crosslinked with formaldehyde to a final concentration of 1.0%.
|
| Growth protocol |
Cells were cultured using DMEM with 10% heat inactivated FBS at 37°C with 5% CO2 in air.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols with a minor modification; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Replicate 1
FoxA1_MCF7_ChIP-exo_ChExMixPeaks.bed
|
| Data processing |
Library strategy: ChIP-exo
For human ChIP-exo assay, Basecalls were performed using Bcl2fastq version 2.16.
For yeast ChIP-exo assay, Basecalls were performed using Bcl2fastq version 2.20.
For human ChIP-exo, reads were aligned to hg19 genome assembly using bwa mem version 0.7.12 for paired reads.
For yeast ChIP-exo, reads were aligned to sacCer3 genome assembly using bwa mem version 0.7.12 for paired reads. The yeast data are just control experiments that are used in simulations in the manuscript.
ChExMix peak caller; https://github.com/seqcode/chexmix
Genome_build: hg19, sacCer3
Supplementary_files_format_and_content: bed, binding events
|
| |
|
| Submission date |
Feb 12, 2018 |
| Last update date |
Feb 13, 2018 |
| Contact name |
Shaun Mahony |
| E-mail(s) |
mahony@psu.edu
|
| Phone |
814-865-3008
|
| Organization name |
Penn State University
|
| Department |
Biochemistry & Molecular Biology
|
| Lab |
Shaun Mahony
|
| Street address |
404 South Frear Bldg
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE110502 |
Characterizing protein-DNA binding event subtypes in ChIP-exo data |
|
| Relations |
| BioSample |
SAMN08520458 |
| SRA |
SRX3684110 |
