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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 11, 2023 |
| Title |
ATAC_B6_HFD_2 [F_B6_1_3] |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
diet: HFD
mouse id: F_B6_1_3
tissue: Liver
replicate: 2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated using a Dounce homogenizer and 1× homogenization buffer (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 1× protease inhibitors (Roche, cOmplete), and 1 mM β-mercaptoethanol). After tissue homogenization, nuclei were recovered by OptiPrep/iodixanol (Sigma-Aldrich) density gradient centrifugation.
Libraries were generated following Omni-ATAC protocol (Corces MR. et al. Nat Methods. 2017;14(10):959-962) with minor adjustments. Nuclei were resuspended in transposition mix (25 µl 2× TD buffer, 2.5 µl transposase, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). After the transposition reaction, DNA was purified with DNA Clean & Concentrator-5 Kit (Zymo Research). Ten microliters of purified transposed DNA were amplified for 9-11 cycles (predetermined) using 25µl of 2 × Ultra II Q5 Master Mix (New England BioLabs) and 1 µl of both amplification primers (Buenrostro JD et al. Nat Methods. 2013;10(12):1213-1218; 1.25 μM final concentration). For cleanup and to remove primer dimers and large (>1,000 bp) fragments from the libraries, SPRIselect beads (Beckman Coulter) were used.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ATAC_F_B6.BigWig
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| Data processing |
For ATAC-seq samples from the C57Bl/6J and 129S1/SvImJ strains reads were trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Alignment was done using to strain-specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.5.4b) with ‘--alignIntronMax 1 --alignEndsType "EndToEnd"’.
Reads were filtered for true pairs and MAPQ>20 with Samtools v 1.9. Duplicates were removed using Picard (v2.8.13) MarkDuplicates.
Peaks were called with HMMRATAC (v1.2.10) using ‘--means 75,200,400,600 --upper 20 --lower 10’.
For F1 samples we used ASEReadCounter* pipeline (https://github.com/gimelbrantlab/ASEReadCounter_star).
Genome_build: mm10
Supplementary_files_format_and_content: Sample-wise peaks: Summits were widened to peaks with Bedtools (v2.27.1) using ‘slop -b 75’. Peaks were shifted to mm10 coordinates using g2gtools. ENCODE blacklisted regions were removed from the regions.
Supplementary_files_format_and_content: Raw counts: Consensus peak set was formed from the peak centers using modified kernel density estimation -based approach (Tuoresmäki et al. PLoS One 2014;9(4):e96105). Reads were shortened to 1bp tags at 5’-ends and counted using csaw (v1.28.0).
Supplementary_files_format_and_content: F1 allelic counts: Counts were obtained from ASEReadCounter* pipeline. Counts were generated using the consensus peak set from ATAC-seq samples from the C57Bl/6J and 129S1/SvImJ strains. The table contains counts for peaks and aggregated counts for SNPs in these peaks.
Supplementary_files_format_and_content: BigWigs: BAM files shifted to mm10 coordinates were downsampled after and merged by group using Samtools. BigWigs were generated using Deeptools (v3.4.2) bamCoverage with '--normalizeUsing CPM --outFileFormat bigwig --binSize 10'.
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| Submission date |
Feb 17, 2022 |
| Last update date |
Dec 11, 2023 |
| Contact name |
Juho Mikael Mononen |
| E-mail(s) |
juho.mononen@uef.fi
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| Organization name |
University of Eastern Finland
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| Department |
Faculty of Health Sciences
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| Lab |
Heikkinen lab
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| Street address |
Yliopistonranta 1E
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| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE196939 |
Genetic determinants of TCF7L2 binding and chromatin availability in mouse liver [ATAC-seq] |
| GSE196942 |
Genetic determinants of TCF7L2 binding and chromatin availability in mouse liver |
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| Relations |
| BioSample |
SAMN26020173 |
| SRA |
SRX14209191 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5905293_ATAC_F_B6_1_3.bed.gz |
212.5 Kb |
(ftp)(http) |
BED |
| GSM5905293_counts_F_B6_1_3.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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