|
Status |
Public on Jan 05, 2016 |
Title |
AZF_rep1, input |
Sample type |
SRA |
|
|
Source name |
HEK293
|
Organism |
Homo sapiens |
Characteristics |
cell type: HEK293 construct: AZF chip-antibody: none
|
Growth protocol |
Stable human embryonic kidney (HEK293) cells expressing either AZF or KLF3FD-AZF were cultured in Dulbecco’s modifieid Eagle’s medium (DMEM) (Cat# 11320-082, Life Technologies) supplemented with 10% fetal bovine serum (Cat# 16000044, Life Technologies), 1% Penicillin-Streptomycin-Glutamate (Life Technologies #10378016) and 2.5ug/ml puromycin (to maintain selection)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Refer to Schmidt D 2009 et al. Methods and Burdach J 2014 et al. NAR. Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP sample prep kit from Illumina, San Diego, CA (Cat #: IP-202-1012).
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Input control
|
Data processing |
Reads were quality filtered, trimmed and adapter sequences were removed using Trimmomatic v0.3.2. Alignment with Bowtie v2.2.1 to the hg19/GRCh37 Homo Sapiens genome. Resulting alignments were sorted and indexed using Samtools v0.1.18. Peak calling with HOMER v.4.7.2. using permissive settings (-P .1 -LP .1 -poisson .1). Peaks lists were supplied to homer-IDR to determine the IDR (irreproducible discovery rate) statistic generating a final peak list satisfying the thresholds set by homer-IDR. Peak calling with HOMER v.4.7.2. using default settings except with (-style factor -F 10). Peak lists were supplied to DIFFBIND v1.10.2 for differential binding analysis. Peak lists were annotated using annotatePeaks.pl using HOMER annotation set for hg19/GRCh37. Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files with peak scores and normalized tag counts.
|
|
|
Submission date |
Jun 10, 2015 |
Last update date |
May 15, 2019 |
Contact name |
WOOI FANG LIM |
E-mail(s) |
wooi.lim@unsw.edu.au
|
Organization name |
University of New South Wales
|
Department |
BABS
|
Lab |
Crossley
|
Street address |
School of Biotechnology and Biomolecular Sciences
|
City |
UNSW Sydney |
State/province |
NSW |
ZIP/Postal code |
2052 |
Country |
Australia |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE69739 |
Genome-wide binding profiles of an artificial zinc finger protein with or without a KLF3 functional domain |
|
Relations |
BioSample |
SAMN03768477 |
SRA |
SRX1055106 |