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Sample GSM541292 Query DataSets for GSM541292
Status Public on Apr 01, 2014
Title RFKO_232
Sample type SRA
 
Source name RFKO_232
Organism Mus musculus
Characteristics strain: C57 BL/6
tissue type: liver
genotype/variation: hs-RXRa-del-exon4-/-
gender: female
antibody: RXRa (D-20)
antibody manufacturer: Santa Cruz Biotechnology
antibody catalog number: sc-553
Extracted molecule genomic DNA
Extraction protocol Genomic DNA were extracted from the cells and fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors followed by Chip treatments of RxRa and Pol II respectively. Sizes between 200 bp (including the adaptors) were selected and sequenced with the Illumina Genome Analyzer II.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description RFKO_232
Data processing Reads are mapped to genome using ELAND. Reads that are uniquely mapped and have no more than 2 mismatches are selected for future analysis. MACS is used to call peaks with p value 1e-10.
 
Submission date May 05, 2010
Last update date May 15, 2019
Contact name deqiang sun
E-mail(s) dsun@tamu.edu
Phone (713) 677-7439
Organization name Texas A&M University
Street address 2121 W Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL9250
Series (2)
GSE21696 Genome-wide analysis of RXRa binding in mouse liver chromatin with ChIP-SEQ.
GSE47899 Genome-wide analysis of liver in male and female mice
Relations
SRA SRX020167
BioSample SAMN00012729

Supplementary file Size Download File type/resource
GSM541292_RFKO_232.export.txt.bed.macs.wig.gz 166.3 Mb (ftp)(http) WIG
GSM541292_RFKO_232.export.txt.gz 928.0 Mb (ftp)(http) TXT
GSM541292_RFKO_232.export.txt.tag2m.bed.macs_peaks.bed.gz 363.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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