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| Status |
Public on Jun 16, 2024 |
| Title |
ATAC-seq of STZ+ SCD mice, 20w, biological replication 3 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
strain: C57BL/6J
age: 20 weeks
streptozotocin treatment: Treated
diet: SCD
Sex: Male
genotype: WT
drug treatment: Untreated
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| Treatment protocol |
Vehicle (HyClone DPBS, Cytiva, Germany) or tirzepatide (109.5 nmol/kg, CPC, Hanzhou, China) dissolved in vehicle was administered via subcutaneous injection to ad libitum-fed STZ+HFD mice 1-2 hours prior to the onset of the dark cycle every 2 days for 10 to 11 weeks.
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| Growth protocol |
Mice were housed in climate-controlled, specific pathogen-free barrier facilities under a 12 h light-dark cycle and provided diet and water ad libitum. They were fed standard chow diet (SCD) (Teklad Global 18% Protein Rodent Diet 2018; Harlan Teklad, WI, USA), 18% fat or HFD (Research Diet (New Brunswick, NJ, USA) D12492, 60% fat) from 8 weeks of age.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq libraries were prepared from 5 mg of fresh liver tissue.
To prepare ATAC-seq library, nuclei were extracted from liver cells using the Singulator 100 system (S2 Genomics, CA, USA) with an extended nuclear dissociation protocol. 50,000 nuclei were transferred to an EP tube containing 1 mL of ATAC-seq resuspension buffer, then transposition solution was adde, and eluted DNA was purified and amplifired with Nextera DNA Flex kit(Illumina).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw ATAC-seq data were trimmed by removing adapters and sequences shorter than 36 base pairs (bp) using TrimGalore (ver. 0.5.0).
Trimmed data were aligned to the mouse genome (mm10, GRCm38) using Bowtie2 (version 2.3.5.1) using the following parameters: -very-sensitive –no-discordant –no-mixed –no-unal.
Mitochondrial reads were subsequently removed using Samtools (version 1.9) and PCR duplicated reads removed using Picard MarkDuplicates tool (Picard version 2.2.2).
Peak calling was performed with MACS2 (version 2.1.1) and ENCODE blacklisted regions for mm10 subtracted with Bedtools intersect (version 2.27.1). Bigwig files were generated using deeptools.
Peaks from MACS2 and sample metadata were inputted into R and read counts for consensus peaksets and overlapping peaks in each sample subsequently counted by R package Diifbind.
Assembly: mm10
Supplementary files format and content: bigWig and bed files containing Peaks generated by ATAC-seq for each sample
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| Submission date |
Oct 25, 2023 |
| Last update date |
Jun 16, 2024 |
| Contact name |
Byung-Kwan Jeong |
| E-mail(s) |
goodididid@gmail.com
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| Organization name |
Asan Medical Center
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| Department |
Pathology
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| Street address |
88, Olympic-ro 43-gil
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| City |
Songpa-Gu |
| State/province |
Seoul |
| ZIP/Postal code |
05505 |
| Country |
South Korea |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE246213 |
A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma [ATAC-seq] |
| GSE246223 |
A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma |
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| Relations |
| BioSample |
SAMN37982007 |
| SRA |
SRX22219333 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7864929_Batch3_STZSCD20w_ATAC_3.bw |
399.6 Mb |
(ftp)(http) |
BW |
| GSM7864929_Batch3_STZSCD20w_ATAC_3.peaks.bed.gz |
443.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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