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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2023 |
| Title |
Adipose 1011-A F |
| Sample type |
SRA |
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| Source name |
adipose
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| Organism |
Mus musculus |
| Characteristics |
tissue: adipose
strain: C57BL/6J
cell type: Adipose - gonadal fat pad
Sex: female
treatment: 10%_fat_+_fiber
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| Treatment protocol |
Male and female mice of each CC founder strain were fed high fat high sugar 45% kcal fat plus 1360% kcal sucrose (Research Diets D19070208) or isocaloric control 10% kcal fat plus 0% kcal sucrose (Research Diets D19072203) diets for 9 weeks prior to tissue harvest and processing for ATAC-seq.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204).
Adipose, liver, and muscle ATAC libraries were constructed as previously described [PMID: 27526324] with a few exceptions. Briefly the protocol entails pelleting and washing cells in cold PBS, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) with the addition of 0.01% digitonin (2x TDE for adipose), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche). Islet ATAC libraries were constructed as previously described [PMID: 34491912] with a few exceptions. Briefly the protocol entails pelleting and washing approximately islets in cold PBS, incubating in ATAC lysis buffer, trituration with 25-gauge needle, centrifugation to generate crude nuclei pellet, washing in ATAC lysis buffer, transposition and adapter addition using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina), DNA purification using the ChIP DNA Clean & Concentrator Kit (Zymo Research), 11 cycle PCR and clean up using KAPA Pure Beads (Roche).
All libraries were sequenced 100 bp paired end on an Illumina NovaSeq 6000.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Mouse raw-reads from the 386 samples described above were quality and adapter trimmed with cutadapt v2.3 . Filtered trimmed reads were mapped with Bowtie2 v2.3.5 [PMID: 22388286]. For C57BL/6J samples, reads were mapped to GRCm38 release 98 (ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz). For all other DO founder strains (A/J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), reads were mapped to strain-specific pseudo-references. Pseudo-references for each strain were constructed with g2gtools v0.1.31 (http://churchill-lab.github.io/g2gtools) by patching GRCm38 release 98 with strain-specific SNPs and Indels from the Mouse Genome Project [PMID: 21921910] REL-1807 (ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/). Mapped reads were filtered to remove PCR duplicates, mtDNA, and the following classes of reads: unmapped, mate unmapped, and non-primary alignment. DeepTools alignmentSieve v3.3.2 [PMID: 27079975] was used to offset all reads aligning to the positive strand by +4bp, and all reads aligning to the negative strand by -5bp to account for Tn5 transposase activity [PMID: 24097267 , PMID: 21143862]. Alignments from non-C57BL/6J samples were then lifted to GRCm38 coordinates with g2gtools. Peak calling was conducted on all pooled alignment files with Macs2 v2.2.7.1 [PMID: 22936215].
Assembly: mm10
Supplementary files format and content: narrowPeak : called peaks of signal enrichment, bed : peaks count matrix, bigwig : read coverage track
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| Submission date |
Jul 31, 2022 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Carol Bult |
| E-mail(s) |
Carol.Bult@jax.org
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| Phone |
207-288-6000
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| Organization name |
The Jackson Laboratory
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| Lab |
The Bult Lab
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| Street address |
600 Main St
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| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE210138 |
Identification of cross-species preserved cis-regulatory elements containing type 2 diabetes GWAS variants |
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| Relations |
| BioSample |
SAMN30071392 |
| SRA |
SRX16743739 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6422275_1011-A_GT20_03840_CCTAAGAC-CTCTCTAT_S35_cat.sorted.rmDup.rmChrM.rmMulti.filtered.shifted.mm10.bigwig |
509.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM6422275_1011-A_GT20_03840_CCTAAGAC-CTCTCTAT_S35_cat_peaks.narrowPeak.gz |
1.5 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM6422275_1011-A_GT20_03840_CCTAAGAC-CTCTCTAT_S35_cat_peaks_countMatrix.mm10.bed.gz |
757.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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