|
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 |