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Sample GSM959055 Query DataSets for GSM959055
Status Public on Feb 13, 2013
Title ChIP-seq_ZFP143_Fibro
Sample type SRA
 
Source name Mouse embryonic fibroblast cell line
Organism Mus musculus
Characteristics cell line: MEF-like
chip antibody: ZNF143, rabbit polyclonal raised against a C-terminal epitope of ZNF143 (Myslinski et al JBC 2006)
Extracted molecule genomic DNA
Extraction protocol ChIP assays were performed essentially as previously described (Myslinski et al. 2006) with 1-4x107 cells. The chromatin was sonicated to an average of 200bp using a BioruptorTM UCD-200 (Diagenode) at Maximum power level for 30 minutes (pulses of 30 seconds with 30 seconds breaks). The immunoprecipitation step was performed with 5µg of specific antibodies. DNA purification steps were done using the MinElute PCR purification kit (Qiagen, cat. No. 28004) or using the classical phenol/chloroform extraction protocol. ChIP-seq library preparation was performed using illumina TruSeq DNA Sample Prep Kits according to manufacturer protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Basecalls performed using Illumina CASAVA version 1.7 or v1.8
ChIP-seq reads were aligned to the hg19 or mm9 genome using Illumina software ELAND or Bowtie v0.12.7.
ChIP-seq peak calling was performed using MACS v1.4
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: Wig files were generated using MACS v1.4 (10bps resolution).
 
Submission date Jul 11, 2012
Last update date May 15, 2019
Contact name PHILIPPE CARBON
Organization name IBMC
Department UPR9002 ARN du CNRS
Street address 15 rue René Descartes
City Strasbourg
ZIP/Postal code 67084
Country France
 
Platform ID GPL11002
Series (1)
GSE39263 Modulation of gene expression by ZNF143, THAP11 and NOTCH1 via overlapping binding sites in mammalian cells
Relations
SRA SRX159137
BioSample SAMN01087348

Supplementary file Size Download File type/resource
GSM959055_ChIP-seq_ZFP143_Fibro.wig.gz 361.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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