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Sample GSM2977054 Query DataSets for GSM2977054
Status Public on May 22, 2018
Title WT2_ChIP
Sample type SRA
 
Source name Brown adipose tissue
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Brown adipose tissue
condition: Cold exposure 4C for 6h
chip antibody: PGC-1α (Millipore, ST1204)
Treatment protocol BL6 mice were exposed to 4C for 6h prior to brown adipose tissue isolation.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared using the SOLiD ChIP-Seq Sample Prep Kit according to the manufacturer’s instruction.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB 5500xl Genetic Analyzer
 
Data processing csfasta and qual raw data files were converted to fastqsanger using Galaxy FastQC; Quality Stats run for each sample
reads aligned with Bowtie for SOLiD V1.1.2 in Galaxy
CHiP-seq peak calls were done with MACS V1.0.1; Peaks meeting FDR < or = 5%  (0.05) were included in the analysis, MFOLD=4
Join V1.0.0 on Intervals-Galaxy
Fetch V4.0.1 closest non-overlapping feature
Slice V0.0.1 bam selects bam fragments within MACS peak intervals from Bowtie alignment
Pileup V1.1.1 to create the pileup dataset
Pileup to Interval-Conversion of single base per row pileup table to an interval dataset
Subtract V1.0.0 intervals- The remaining intervals are present only in the dataset from which the subtraction was done.
Genome_build: GRC38/mm10
Supplementary_files_format_and_content: bedgraph-chromosome, start, end, dataValue
 
Submission date Feb 02, 2018
Last update date May 22, 2018
Contact name Ji Suk Chang
Organization name Pennington Biomedical Research Center
Department Gene Regulation and Metabolism
Street address 6400 Perkins Rd.
City Baton Rouge
State/province LA
ZIP/Postal code 70808
Country USA
 
Platform ID GPL15907
Series (2)
GSE110053 A map of the PGC-1α- and NT-PGC-1α-regulated transcriptional network in brown adipose tissue [ChIP-Seq]
GSE110056 A map of the PGC-1α- and NT-PGC-1α-regulated transcriptional network in brown adipose tissue
Relations
BioSample SAMN08457582
SRA SRX3643057

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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