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Sample GSM1234315 Query DataSets for GSM1234315
Status Public on May 16, 2014
Title J1_Ino80KD_Klf4
Sample type SRA
 
Source name cell line
Organism Mus musculus
Characteristics cell line: J1
antibody: Klf4
vendor/catalog#: R&D, AF3158
transfection: lentiviral mediated-shRNA against non-targeting Ino80
Growth protocol J1 cell were maintianed in ESGRO medium. Cell were cultured in M15 medium when ChIP was performed.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde, sonicated and precipitated by Ino80, Oct4, Klf4, Med1, or Pol2 antibodies. Then precipitated DNA was reverse crosslinked, extracted and quantified for library.
Library was prepared by TruSeq DNA Sample Prep kit (Illumina) or Nextera XT DNA sample prep kit (Illumina) according to the manufacturer's protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description Library was prepared by Nextera XT kit
Data processing Basecalls performed using CASAVA version 1.7
Raw data from the replicates were merged.
Raw data was filtered by the following steps: reads were filtered if the average base quality score <20 and duplicate reads removed (based on identical sequences)
Reads were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bowtie (v0.12.8 using the following parameters: -v 2 -m 1)
Mapped data was filtered to remove hits with >2 mismatches to the reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file per sample per strand showing normalized mapped read coverage; generated by BEDtools genomeCoverageBed and bedGraphToBigWig.
Supplementary_files_format_and_content: Ino80 peak bed files were generated by SICER v1.1 (redundancy threshold=1, window size=200, gap size=800, fragment size=300, FDR=1e-6)
 
Submission date Sep 18, 2013
Last update date May 15, 2019
Contact name Li Wang
Organization name NIH
Street address 111 T.W. Alexander Dr
City Durham
ZIP/Postal code 27709
Country USA
 
Platform ID GPL16417
Series (1)
GSE49137 INO80 complex in the core regulatory network governing ESC self-renewal [ChIP-Seq]
Relations
BioSample SAMN02359191
SRA SRX355580

Supplementary file Size Download File type/resource
GSM1234315_J1_Ino80KD_Klf4.bw 111.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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