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Sample GSM3703245 Query DataSets for GSM3703245
Status Public on Oct 21, 2019
Title H3K27ac_ZT12 control REP2
Sample type SRA
Source name H3K27ac_ZT12 control
Organism Mus musculus
Characteristics strain: C57BL/6J
treatment: 12 wk control Diet (Research Diet, D12329)
tissue: Liver
time: ZT12
chip antibody: GR (Santa Cruz, sc-1004X)
Extracted molecule genomic DNA
Extraction protocol ChIP was performed as previously described (Uhlenhaut et al. 2012). Briefly, 100 mg of frozen liver was minced and Dounce homogenated in 0.7 mg/mL DSG crosslinker and 1% Formaldheyde. Nuclei were isolated and chromatin sonicated to a 1-0.1 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies.
Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Data processing Mapping against mm9 mouse genome using bwa 7.12
Duplicate removal using samtools v2.4.0 and Downsampling
Peak calling with macs2 version 2.1.1
IP efficiency normalization
Create normalized peak universe
Genome_build: mm9
Supplementary_files_format_and_content: broadpeak and gappedPeak files were produced using macs2 representing H3K27ac peaks
Submission date Apr 02, 2019
Last update date Oct 22, 2019
Contact name Nina Henriette Uhlenhaut
Organization name HelmholtzZentrum München - IDC
Department Molecular Endocrinology
Lab Uhlenhaut IDC
Street address Ingolstädter Landstraße 1, Neuherberg
City Munich
State/province Bavaria
ZIP/Postal code D-85764
Country Germany
Platform ID GPL17021
Series (2)
GSE108690 Cistromic reprogramming of the diurnal glucocorticoid hormone response by high fat diet
GSE129230 GR cistromes reprogramming by High Fat Diet [ChIP-seq H3K27ac]
BioSample SAMN11318560
SRA SRX5625521

Supplementary file Size Download File type/resource
GSM3703245_GAR1766_CL4_2_peaks.broadPeak.gz 1.1 Mb (ftp)(http) BROADPEAK
GSM3703245_GAR1766_CL4_2_peaks.gappedPeak.gz 1.6 Mb (ftp)(http) GAPPEDPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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