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Sample GSM1479734 Query DataSets for GSM1479734
Status Public on Dec 31, 2016
Title H3K27ac ZT 18 Bmal1 KO
Sample type SRA
 
Source name Liver, Bmal1 KO, ZT 18, H3K27ac ChIP
Organism Mus musculus
Characteristics strain/background: C57/BL6
genotype/variation: Bmal1 KO
gender: male
feeding: night-restricted feeding
tissue: liver
time point: ZT 18
technique: H3K27ac ChIP-seq
chip antibody: anti-H3K27ac
Growth protocol C57/BL6 male, 12- to 14-wk-old (at time of sacrifice) mice were housed in a 12 h light/12 h dark (LD) regimen for 2 wk with water and food available ad libitum. They were then phase-entrained to a 12 h/12 h LD regimen with water ad libitum but food access between ZT12 and ZT24 for 7 d (ZT, Zeitgeber time; ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off). At each ZT2, ZT06, ZT10, ZT14, ZT18, ZT22, and ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 2 ml of PBS through the spleen and immediately collected. A small piece of liver tissue (approx. 100 mg) was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The remaining liver tissue was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation. All animal care and handling was performed according to the State of Geneva's law for animal protection.
Extracted molecule genomic DNA
Extraction protocol ChIP-seq H3K27ac protocol: ChIPs were performed according to the method described by Reddy et al. (2009) with a few modifications. The 100 ul chromatin aliquots were used for each IP and diluted with 900 ul of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS at pH 7.4) and added to dynal magnetic beads conjugated with (sheep anti-mouse IgG Dynabeads, Invitrogen, Cat no: 110-31) pre-treated with 3 ul of polyclonal antibody for H3K27ac (Active Motif, Cat no: 39135) for immunoprecipitation of specific complexes. The samples were incubated overnight at 4°C on rotator, then magnetic beads washed 7 times with lithiumchloride wash buffer (100mM Tris at pH 7.5, 500mM LiCl, 1% NP-40 and 1% sodiumdeoxycholate) and finally once with 1X TE buffer (10mM Tris-HCl at pH 7.5, 0.1mM Na2EDTA). The chromatin complex was eluted using elution buffer (1% SDS, 0.1M NaHCO3) for 1 h at 65°C using eppendorf thermo-mixer. The chromatin was then de-crosslinked overnight at 65°C and ChIP DNA purified using Qiagen PCR purification kit and eluted in 50 ul of elution buffer. For qPCR reaction, 1.5 ul of 1/10 diluted ChIP DNA is used.
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 HiSeq 2500
 
Description Chromatin
Data processing All alignments were performed using the BBCF HTSstation (available at http://htsstation.epfl.ch , David et al., 2014).
Peak calling was done using ChIP-peak (Schmid CD, Bucher P. 2010, Ambrosini G., Dreos R. and Bucher P. IWBBIO 2014, Available: http://ccg.vital-it.ch/chipseq/chip_peak.php) on DNase signal using all ZT concatenated with the following parameters: cutoff=100,vicinity=400,window size=600, threshold=1000. A peak calling was done as well specifically for ZT6 in the WT and in the Bmal1KO context with the following parameters: cutoff=100,vicinity=1000,window size=600, threshold=200. Detected peaks were quantified using the DNase and PolII signal with a window of +/-300 bp around peak center and using the H3K27ac with a window of +/-1kb peak center for each time point and in each context.
Wig files were generated using bam2wig (see David et al., 2014) and were normalized according to the number mapped reads divided by 10e7. DNase I signal is represented using the first position of the reads considered as the cutting position and without strand shifting. Pol II and H3K27ac are represented using the whole read length and a shift of respectively 80bp and 90bp for PolII and H3K27ac.
DNase hypersensitive sites footprints were detected using Wellington algorithm (Piper et al. 2013) with the following parameters: -sh 20,36,5 -fdr 0.05
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Processed data files contain the normalized signal for each mark at each time point in BigWig format. In addition, the DNaseI hypersensitive peaks detected by the peak calling tool are provided in BigBed format. The footprints detected by Wellington algorithm are provided in BigWig format where the footprint score is reproted in negative scale (see Piper 2013). A table of quantile-normalized quantification of each mark at each time point and in WT and Bmal1KO context is provided in text format.
 
Submission date Aug 14, 2014
Last update date May 15, 2019
Contact name Jonathan Aryeh Sobel
E-mail(s) jonathan.sobel@epfl.ch
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 GPL17021
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
Relations
BioSample SAMN02990961
SRA SRX681525

Supplementary file Size Download File type/resource
GSM1479734_BMAL1KO_H3K27ac_ZT18.bw 496.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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