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| Status |
Public on Nov 18, 2024 |
| Title |
ATAC_URF_3 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: wt
treatment: unrestricted feeding
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| Growth protocol |
Mice were subjected to either a 4-week alternate day fasting (ADF) regimen or unrestricted feeding (URF). At the end of the experiment mice were divided to 3 groups: the first group was euthanized after a 24 h fasting period (ADF_f or URF_f). The second group fasted for 24 h followed by ad libitum refeeding for 24 h at the end of which they were euthanized (ADF_re or URF_re). The third group did not experience any type of fasting (unrestricted feeding). Each group has 3 replicates.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To isolate nuclei, liver samples (50 mg) were homogenized in hypotonic sucrose buffer (250 mM sucrose, 10 mM Tris-Hcl pH 7.8, 0.1% Igepal, 3mM MgCl2, 10mM KCl, 0.2 mM Dithiothreitol, 0.5 mM spermidine, protease inhibitor cocktail) in a dounce homogenizer. Homogenate was filtered through a 20 µM filter, spun and washed (10 mM Tris-Hcl pH 7.5, 3 mM MgCl2, 10 mM NaCl, 0.1% tween-20). 50,000 nuclei were included for next steps as described (Korenfeld et al., 2023). Each sample was sequenced at a depth of at least 50X10^6 reads (paired-end).
ATAC-seq libraries were prepared using specific DNA Barcodes and Q5 High-Fidelity DNA Polymerase from New England Biolabs. Libraries were amplified using 13 cycles on the thermocycler. PCR-amplified DNA was purified using a MinElute PCR purification kit from Qiagen following manufacturer’s instructions. Post amplification libraries were size selected at 150-400nt in length using magnetic AMPure XP beads from Beckman Coulter.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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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 |
Sep 23, 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 |
GPL21626 |
| Series (1) |
| GSE212776 |
Repeated fasting events sensitize chromatin and gene expression to support augmented ketogenesis |
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| Relations |
| BioSample |
SAMN43889032 |
| SRA |
SRX26173281 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8530727_TD_female_urf_3.ucsc.bedGraph.gz |
500.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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