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Sample GSM4089006

Query DataSets for GSM4089006

Status

Public on Sep 02, 2020

Title

HFD_Diet_input_KO_2

Sample type

SRA

Source name

Knockout Mouse fed high fat diet for 12 weeks

Organism

Mus musculus

Characteristics

strain: C57BL6/J
genotype: PPARg knockout
gender: male
age: 5 months
tissue: liver
treatment: High Fat Diet
chip antibody: none - not applicable

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