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| Status |
Public on Nov 27, 2019 |
| Title |
ARID3A |
| Sample type |
SRA |
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| Source name |
HepG2 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
chip antibody: ARID3A
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| Growth protocol |
HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Re-analysis of:
GSM935275
Raw file(s):
ENCFF000XOS ENCFF000XOU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000EDP
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| 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.
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| Submission date |
Sep 29, 2017 |
| Last update date |
Nov 27, 2019 |
| Contact name |
Eric M Mendenhall |
| E-mail(s) |
emendenhall@hudsonalpha.org
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| Organization name |
HudsonAlpha Institute
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| Lab |
Mendenhall Lab
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| Street address |
601 Genome Way Northwest
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| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE104247 |
Genome-wide TFBS (Transcription Factor Binding Site) map analysis in HepG2 cells |
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| Relations |
| BioSample |
SAMN07718440 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2797484_ARID3A_human_IDR0.02_narrowPeak.bed.gz |
256.9 Kb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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