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Sample GSM4512857 Query DataSets for GSM4512857
Status Public on May 04, 2020
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: liver
chip antibody: none
time point: ZT 14
Growth protocol Mice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum. ZT0 is defined as the time when the lights are turned on. Animals were housed for 3 weeks under the indicated photoperiods.
Extracted molecule genomic DNA
Extraction protocol For the HSF1 ChIP-Seq, chromatin preparation and chromatin immunoprecipitation were performed as in Rey et al., PLoS Biol 2011. The HSF1 polyclonal antibody is from Stressgen (Enzo Life Sciences). For each IP, 5ul of HSF1 antibody was used with 250ul of pre-cleared chromatin.
Libraries for ultra-high throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Input DNA
Data processing Alignment: Sequence reads were aligned to the mouse genome (mm9) using BWA software
bigwig were produced using deeptools bamCoverage command with the following parameters: --centerReads --extendReads 37
HSF1peaks were analysed using Macs2 with default parameters with a p-value threshold below 0.001 and annotated with the closest gene using Chippeakanno R package.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig, anannotated Macs2 peaks in txt format
Submission date May 04, 2020
Last update date May 07, 2020
Contact name Jonathan Aryeh Sobel
Organization name EPFL
Department School of Life Sciences
Lab Felix Naef Lab
Street address EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15
City Lausanne
State/province Vaud
ZIP/Postal code CH-1015
Country Switzerland
Platform ID GPL9185
Series (2)
GSE60430 Regulatory logic of the coupled diurnal and feeding cycles in the mouse liver [DNase-seq, ChIP-seq]
GSE60578 Regulatory logic of the coupled diurnal and feeding cycles in the mouse liver
BioSample SAMN14827291
SRA SRX8244938

Supplementary file Size Download File type/resource 106.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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