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Sample GSM3317129 Query DataSets for GSM3317129
Status Public on Aug 02, 2018
Title ZT4 mouse2
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics chip antibody: HNF4A
strain: C57BL/6
tissue: liver
age: 8-week old
Extracted molecule genomic DNA
Extraction protocol ~ 50 mg of blood perfused liver tissue were dissected from C57BL/6J mice, snap frozen in liquid nitrogen and stored at -80°C. Frozen liver tissues were minced in ice-cold PBS using razor blades into 1 mm cubed, and then homogenized by pushing through 1.5-inch 18G needle for 10 times and then 1.5-inch 21G needle for 20 times. Homogenized cells were immediately crosslinked with 1% formaldehyde for 10 min. The crosslink was quenched by adding glycine to a final concentration of 125 μM. After two washes with cold PBS, the nuclei were lysed in 150 μl nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) containing 1x EDTA-free protease inhibitor cocktail (Roche), by keeping on ice for 5 min. Immediately, to fragment the chromatin, the lysates were sonicated 17 times for 30 sec by using Bioruptor (Diagenode). After centrifuged at 17,000 rpm for 15 minutes at 4°C, the 150 μl fragmented chromatin was diluted 10-fold with IP dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 1 mM EDTA) supplemented with 1x EDTA-free protease inhibitor cocktail, and then incubated with 7 μg anti-HNF4A (abcam cat. ab41898) overnight at 4°C. 100 μl of Dynabeads Protein G (Invitrogen cat. #10004D) was added to the chromatin and incubated for another 3 h. Afterwards, the beads were washed once with low salt wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA) and once with high salt wash buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA). 200 μl of IP elution buffer (1% SDS, 100 mM NaHCO3) was applied to the bead pellet and incubated at 30°C for 15 min. The eluate was added with 5M NaCl to final conc. of 200 mM and reverse-crosslinked at 65°C overnight. To remove RNA and protein, RNase A and proteinase K were subsequently applied by incubating at 45°C for 1 h. Finally, we diluted the DNA with 5 volumes of Qiagen buffer PB (QIAquick PCR Purification Kit) and purified with QIAquick PCR Purification columns. We eventually resolved our DNA fragments in 30 μl Qiagen Buffer EB.
For library preparation, 2 ng of each sample was prepared using the NEB Ultra DNA Library Prep Kit for Illumina following manufacturer’s instructions. Each library was dual size selected with 0.55X and 0.14X Ampure beads followed by PCR amplification with Kappa HiFi 2x PCR mix (15 cycles). PCR product was then quantitated using the Qubit (Thermo Fisher) and BioAnalyzer (Agilent BioAnalyzer 2100) to determine library quantity. Libraries were then gel purified on a 2% agarose gel to remove secondary PCR amplification artifacts, quantitated on the Qubit and loaded onto a NextSeq500 flowcell for 1 x 76 base single-end sequencing to generate approximately 20M reads per sample.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description ZT4
HNF4A ChIP-seq
Data processing Illumina SE 75 bp reads produced by HNF4A ChIP-Seq on C57BL/6 mouse liver were mapped to the mouse mm9 genome using Bowtie2 with the following parameters: -N 1
Peak calling for HNF4A ChIP-seq was performed with PePr with the following parameters: --threshold 1e-2 --peaktype sharp.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using HOMER (v4.10) with default parameters.
 
Submission date Aug 01, 2018
Last update date Aug 03, 2018
Contact name Meng Qu
E-mail(s) marciaqu@gmail.com
Phone 626-898-2391
Organization name University of Southern California
Department Keck Medical School
Lab Steve Kay lab
Street address 1002 West Childs Way
City Los Angeles
State/province California
ZIP/Postal code 90089
Country USA
 
Platform ID GPL19057
Series (1)
GSE118007 Characterization of genome-wide DNA binding rhythms of HNF4A
Relations
BioSample SAMN09755400
SRA SRX4497833

Supplementary file Size Download File type/resource
GSM3317129_ZT4_2_S5_R1_001.ucsc.bedGraph.gz 153.9 Mb (ftp)(http) BEDGRAPH
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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