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| Status |
Public on Nov 18, 2024 |
| Title |
chip, urf_f_2 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: wt
treatment: 24h fasting
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Liver pieces (150 mg) were cross-linked with phosphate-buffered saline (PBS) containing 2mM disuccinimidyl glutarate (DSG, Santa Cruz Biotechnology, cat# sc-285455). Livers were homogenized with a Dounce homogenizer and rotated for 30 min at room temperature. Crosslinked samples were washed in phosphate buffered saline (PBS), resuspended in ChIP lysis (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH8) buffer and sonicated to release 100-1000 bp fragments. Antibody against PPARa was conjugated to magnetic beads for 2 h at 4°C. Chromatin was immunoprecipitated with antibody-bead conjugates for 16 h at 4°C. Immunocomplexes were washed sequentially with the following buffers:low salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl), high salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 500 mM NaCl), LiCl buffer (0.25M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid, 1mM EDTA, 10 mM Tris pH 8.1) and twice with TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8). Chromatin was eluted, de-crosslinked for 4 h at 65°C and deproteinized with proteinase K (Hy Labs, cat# EPR9016) for 1 h at 50°C..DNA was subsequently isolated using MinElute DNA purification kit.
ChIP DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10
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| Submission date |
Mar 22, 2024 |
| Last update date |
Nov 18, 2024 |
| Contact name |
Ido Goldstein |
| Organization name |
The Hebrew University of Jerusalem
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| Department |
Institute of Biochemistry, Food Science and Nutrition
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| Street address |
POB 12
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE212776 |
Repeated fasting events sensitize chromatin and gene expression to support augmented ketogenesis |
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| Relations |
| BioSample |
SAMN40583790 |
| SRA |
SRX24027937 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8161062_TD_urf_f_3.ucsc.bedGraph.gz |
121.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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