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| Status |
Public on Jan 28, 2018 |
| Title |
Day5_IL10 |
| Sample type |
SRA |
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| Source name |
iBAd Cell Line
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| Organism |
Mus musculus |
| Characteristics |
strain: C57/Bl6
genotype: IL10Ra-Expressing
stimulus: With IL-10 and Isoproterenol
time point: Day5
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 iBAd cells on Day 0 and Day 5 of differentiation were centrifuged and washed once with PBS prior to addition of 50uL cold hypotonic lysis buffer containing 0.1% Igepal to yield nuclei. The lysis reaction was centifuged and the supernatant was discarded. Isolated nuclei were incubated with 2.5uL Tn5 (Nextera) in a 50uL reaction volume and placed in a 37C waterbath for 30 minutes.
All ATAC datasets were generated using Tn5 from Nextera with previously published protocols with minor adjustments (Buenrostro et al, Curr.Protoc. Mol. Biol. 2015). Transposed DNA was cleaned up with a Qiagen MinElute PCR Purification Kit and amplified with a non-saturating PCR to enrich for Transposed DNA. The reaction was size selected on a gel for fragments 100-1000bp, were quantified with qPCR and Qubit, and sequenced 50bp, single-end sequencing.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Library strategy: ATAC-Seq
ATAC-seq libraries were sequenced on an Illumina HiSeq 2000.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23
All fastq files were mapped using bowtie2 and reads were removed if they were non-unique, in duplicate, mapped to mitochondrial genome, or mapped to un-mapped contiguous sequences. Only the remaining reads following these filters were used for subsequent analysis.
bedGraph files were geenrated from sorted bam files using makeTagDirectories and makeUCSCfile with -fragLength 60 -o auto -fsize 1e50 -res 1
MACS2 was used to perform peak calling with the following parameters:--nomodel -g mm --keep-dup all -q .01 --llocal 1000. Peaks from all samples were collapsed and merged together. Reads were quantified using Seqmonk over all peaks and converted to Reads Per Million by dividing the reads by the the total number of reads per sample while normalizing for the length of the peak.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files for each sample represent the read coverage at each genomic position
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| Submission date |
Feb 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Tontonoz |
| Organization name |
UCLA
|
| Department |
Pathology
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| Lab |
Tontonoz Lab
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| Street address |
675 Charles E Young
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE94651 |
IL-10 signaling remodels adipose chromatin architecture to limit thermogenesis and energy expenditure [ATAC-Seq] |
| GSE94654 |
IL-10 signaling remodels adipose chromatin architecture to limit thermogenesis and energy expenditure |
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| Relations |
| BioSample |
SAMN06311409 |
| SRA |
SRX2544220 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2480370_Day5_IL10.bedGraph.gz |
162.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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