|
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 |