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Sample GSM1479716 Query DataSets for GSM1479716
Status Public on Dec 31, 2016
Title PolII ZT 2 Bmal1 KO
Sample type SRA
 
Source name Liver, Bmal1 KO, ZT 2, PolII ChIP
Organism Mus musculus
Characteristics strain/background: C57/BL6
genotype/variation: Bmal1 KO
gender: male
feeding: night-restricted feeding
tissue: liver
time point: ZT 2
technique: PolII ChIP-seq
chip antibody: anti-PolII
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 PolII protocol: Perfused livers were processed for chromatin preparation as described in Ripperger JA, Schibler U (2006). The chromatin samples from the five mice were then pooled, frozen in liquid nitrogen, and stored at -80°C. For the ChIP experiments, the following antibody was used: anti-RPB2 (Santa Cruz Biotechnology, sc-673-18). To determine the optimal amounts of antibody, we performed pilot ChIP assays and determined the enrichment for a set of promoters by real-time qPCR according to Ripperger JA, Schibler U (2006). A total of 1 ml of each chromatin suspension (containing about 60 µg of DNA) was incubated with 10 µg of anti-RPB2 in buffer A (20 mM Tris/HCl (pH 7.5), 150 mM NaCl, 2 mM EDTA) overnight at 4°C on a rotating wheel. Ten µl of protein A bead suspension (25% slurry in buffer A), pre-blocked with 10 µg/ml of salmon sperm DNA and BSA at 4°C overnight, was then added and the incubation was continued for 1 h at room temperature on a rotating wheel. The beads were then washed with dialysis buffer and ChIP wash buffer as described in O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ (2006). Protein-DNA complexes were eluted from the beads, de-cross-linked, and treated with RNase A and, subsequently, with proteinase K, as described in O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ (2006). The DNA concentration was determined by fluorometry on the Qubit system (Invitrogen). A total of 10-12 ng DNA were used for the preparation of the library.
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 SAMN02990943
SRA SRX681507

Supplementary file Size Download File type/resource
GSM1479716_BMAL1KO_Pol2_ZT02.bw 469.2 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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