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Sample GSM2911265 Query DataSets for GSM2911265
Status Public on Oct 21, 2019
Title GR_ZT20 control REP2
Sample type SRA
 
Source name GR_ZT20 control_liver
Organism Mus musculus
Characteristics strain: C57BL/6J
treatment: 12 wk control Diet (Research Diet, D12329)
tissue: Liver
chip antibody: GR (Santa Cruz, sc-1004X)
Extracted molecule genomic DNA
Extraction protocol ChIP was performed as previously described (Uhlenhaut et al. 2012). Briefly, 200 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 1-0.5 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: narrowpeak files were produced using macs2 representing GR peaks
 
Submission date Jan 03, 2018
Last update date Oct 21, 2019
Contact name Nina Henriette Uhlenhaut
E-mail(s) henriette.uhlenhaut@helmholtz-muenchen.de
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)
GSE108689 GR cistromes reprogramming by High Fat Diet [ChIP-seq: GR day/night]
GSE108690 Cistromic reprogramming of the diurnal glucocorticoid hormone response by high fat diet
Relations
BioSample SAMN08287070
SRA SRX3582915

Supplementary file Size Download File type/resource
GSM2911265_GR_BL6-2_peaks.narrowPeak.gz 67.6 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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