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Sample GSM2797486 Query DataSets for GSM2797486
Status Public on Nov 27, 2019
Title ARID5B
Sample type SRA
 
Source name HepG2 cells
Organism Homo sapiens
Characteristics cell line: HepG2
chip antibody: FLAG-ARID5B
Growth protocol HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)
Extracted molecule genomic DNA
Extraction protocol Cross-linked chromatin was immunoprecipitated with an antibody. The Protein:DNA crosslinks were then reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and go to http://hudsonalpha.org/myers-lab/protocols for the most current version of the protocol.
Illumina Single End for ChIP-seq
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Fastq files were downloaded from ENCODE portal (https://www.encodeproject.org/) for 2 replicates and 2 controls
ChIP-seq fastqs and ChIP-seq controls were aligned to hg19 genome assembly using BWA-0.7.12(Burrows Wheeler Aligner)
Post-alignment filtering was performed using samtools with MAPQ_THRESH=30 & picard-tools-1.88 to remove the duplicates
Peak enrichment was computed using phantompeakqualtools, implementing SPP peak calling algorithm, to generate narrowpeaks
IDR was run on replicates peak file and pooled peaks, using idr-2.0.2 tool, to generate peaks passing IDR cutoff 0.02 (soft-idr-threshold) followed by filtering of ENCODE blacklisted regions
Genome_build: hg19 male
Supplementary_files_format_and_content: NarrowPeak files are in BED6+4 format with 10 tab-delimited columns [chrom ,chromStart ,chromEnd ,name ,score ,strand ,signalValue ,pValue(-log10) ,qValue(-log10) , peak]; -1 used if no pValue, qValue assigned.
 
Submission date Sep 29, 2017
Last update date Nov 27, 2019
Contact name Eric M Mendenhall
E-mail(s) emendenhall@hudsonalpha.org
Organization name HudsonAlpha Institute
Lab Mendenhall Lab
Street address 601 Genome Way Northwest
City Huntsville
State/province AL
ZIP/Postal code 35806
Country USA
 
Platform ID GPL18573
Series (1)
GSE104247 Genome-wide TFBS (Transcription Factor Binding Site) map analysis in HepG2 cells
Relations
BioSample SAMN07718487
SRA SRX3230377

Supplementary file Size Download File type/resource
GSM2797486_ARID5B_FLAG_IDR0.02_narrowPeak.bed.gz 653.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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