|
| Status |
Public on Jan 05, 2016 |
| Title |
KLF3FD_rep1, input |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293
construct: KLF3FD
chip-antibody: anti-V5 antibody (Cat# R960CUS, Life Technologies)
|
| Growth protocol |
Stable human embryonic kidney (HEK293) cells expressing either, KLF3FD, 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 NextSeq 500 |
| |
|
| 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 sapienss 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 |
Oct 01, 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 |
GPL18573 |
| Series (1) |
| GSE69739 |
Genome-wide binding profiles of an artificial zinc finger protein with or without a KLF3 functional domain |
|
| Relations |
| BioSample |
SAMN04125352 |
| SRA |
SRX1299481 |
