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Sample GSM717566 Query DataSets for GSM717566
Status Public on Apr 30, 2011
Title M21-CBP
Sample type SRA
 
Source name Mutant liver
Organism Mus musculus
Characteristics tissue: liver
chip antibody: CBP
Extracted molecule genomic DNA
Extraction protocol Native chromatin without cross-linking was released from nuclei by incubation in the buffer containing 0.1 N CaCl2, and then digested with MNase for 15 min (partial digestion) and 30 min (full digestion). Mononucleosomal DNA was collected and pooled from both partial and full digestion of four mouse livers. Mononucleosomal and undigested genomic DNA were purified with the Qiagen PCR purification kit after the digestion with protease K. For DNA sequencing, nucleosomal DNA was further modified following the Illumina sequencing protocol and sequenced with an Illumina Genome Analyzer. For ChIP-Seq, after crosslinking, chromatin was sonicated to reduce the size of DNA to 100~1,000 bp, which was further modified for Illumina sequencing as described above.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description CBP binding in mutant liver
Data processing We obtained approximately 124 millions reads of 36 nt uniquely aligning to mouse genome (mm8, UCSC genome database). Then, we extended 36 nt reads to 120 bp based on the average size of nucleosomal DNA fragments. Nucleosome positions were defined as genomic regions containing at least four extended reads, based on the average reads at each sequencing locus with 20% FDR. ChIP-Seq binding regions were identified with an input-directed algorithm GLITR.
 
Submission date Apr 29, 2011
Last update date May 15, 2019
Contact name Jonathan Schug
E-mail(s) jschug@pennmedicine.upenn.edu
Phone 215 898 0773
Organization name University of Pennsylvania
Department School of Medicine
Lab Next-Generation Sequencing Core
Street address 12-156 Smilow Ctr Trans Research
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104-5160
Country USA
 
Platform ID GPL9185
Series (1)
GSE26729 The Nucleosome Map of the Mammalian Liver
Relations
SRA SRX059746
BioSample SAMN00262622

Supplementary file Size Download File type/resource
GSM717566_FGC0130_s_4_ucsc.bed.gz 290.8 Mb (ftp)(http) BED
GSM717566_kkzl_130_4_rd_v_none_10_glitr.bed.gz 46.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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