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| Status |
Public on Nov 18, 2024 |
| Title |
atac, urf_re, 2 |
| Sample type |
SRA |
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| Source name |
liver tissue
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: C57BL/6JOlaHsd
treatment: urf_re
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| Treatment 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 two 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 control for each fasting state is the re-feeding group. Each group has 3 replicates.
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| Growth protocol |
Female, 6 weeks-old mice (C57BL/6JOlaHsd) were randomly assigned to either the URF or ADF groups (12 mice per group). The experiment started after 1 week of acclimation. The URF group had ad libitum access to food (Teklad TD2018) and water for 30 days. The ADF group had ad libitum access to food and water for 24 h followed by ad libitum access to only water for 24 h.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA-seq: Total RNA was isolated from liver pieces (30 mg) using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol. ATAC-seq: To isolate nuclei, liver samples (10 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 (Corces et al., 2017). Each sample was sequenced at a depth of at least 50X106 reads (paired-end).
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421). ATAC DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Binary Base Call (BCL) output files from a Nextseq 500 machine were converted to FASTQ format, using BCL to FASTQ (bcl2fastq v2.20.0.422 Copyright (c) 2007-2017 Illumina, Inc.).
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10
Supplementary files format and content: bedGraph
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| Submission date |
Sep 06, 2022 |
| 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 |
SAMN30686743 |
| SRA |
SRX17444866 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6547585_TD_female_urf_re_2.ucsc.bedGraph.gz |
418.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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