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Sample GSM4088991 Query DataSets for GSM4088991
Status Public on Sep 02, 2020
Title Control_Diet_RXR_KO_2
Sample type SRA
 
Source name Knockout Mouse fed control diet for 12 weeks
Organism Mus musculus
Characteristics strain: C57BL6/J
genotype: PPARg knockout
gender: male
age: 5 months
tissue: liver
treatment: Control Diet
chip antibody: RXR antibody (sc-774 )
Treatment protocol Mice were fed either control diet or high fat diet supplemented with Pio or vehicle.
Extracted molecule genomic DNA
Extraction protocol As described in Huang et al., Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition, Epigenetics, 2015. PubMed: 25482284
As described in Huang et al., Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition, Epigenetics, 2015. PubMed: 25482284
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Data processing Basecalls performed using RTA Version 2.7.3
ChIP-seq reads were aligned to the mm10 genome assembly using novoalign version V3.04.06 with harclipping (-H) and adapter stripping (-a)
Peaks were called using MACS version version 2.1.1 (20160309) using a paired input control
Genome_build: mm10
Supplementary_files_format_and_content: Bed files: The bed files contain the called peaks, the 5th column is the standard MACS -10*log10pvalue; Xls files: contain the peaks with additional information, such as position of peak summit, number of tags in peak region, fold enrichment and FDR
 
Submission date Sep 22, 2019
Last update date Sep 02, 2020
Contact name Paul Cliften
E-mail(s) pcliften@wustl.edu
Organization name Washington University
Department Genetics
Lab GTAC
Street address 4320 Forest Park Parkway
City St. Louis
ZIP/Postal code 63108
Country USA
 
Platform ID GPL21493
Series (1)
GSE137820 Pioglitazone induces extensive PPARg-dependent hepatic expression of nuclear-mitochondrial genes
Relations
BioSample SAMN12816685
SRA SRX6886003

Supplementary file Size Download File type/resource
GSM4088991_2_control_rxr_minus_32_control_input_peaks.narrowPeak.gz 415.4 Kb (ftp)(http) NARROWPEAK
GSM4088991_2_control_rxr_minus_32_control_input_peaks.txt.gz 484.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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