|
| Status |
Public on Jun 09, 2020 |
| Title |
28249_ZEB2_K562 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
antibody: '2A11'
|
| Treatment protocol |
MCF7 cells were additionally grown in phenol red-free DMEM and treated with Beta-estradiol 30 min prior to cell harvest.
|
| Growth protocol |
K562 were grown in suspension using IMDM media and periodically checked for mycoplasma contamination. HepG2 and MCF7 were grown as adherent cells in DMEM media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; 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 |
26290-28249_peak.bed
|
| Data processing |
Library strategy: ChIP-exo
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1) -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
peaks were called using ChExMix version: 0.45 with the following setting: q-value (0.1)
Genome_build: hg19
Supplementary_files_format_and_content: bed format, ChExMix peak calls
|
| |
|
| Submission date |
May 27, 2020 |
| Last update date |
Jun 09, 2020 |
| Contact name |
B. Franklin Pugh |
| E-mail(s) |
fp265@cornell.edu
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
B. Franklin Pugh
|
| Street address |
465 Biotechnology Bldg.
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE151287 |
Screening of PCRP transcription factor antibodies in biochemical assays |
|
| Relations |
| BioSample |
SAMN15037217 |
| SRA |
SRX8407622 |
