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Sample GSM1900121 Query DataSets for GSM1900121
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 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
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
BioSample SAMN04125352
SRA SRX1299481

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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