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| Status |
Public on Jul 27, 2021 |
| Title |
C2C12_UnT_2 |
| Sample type |
SRA |
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| Source name |
C2C12 myotubes
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| Organism |
Mus musculus |
| Characteristics |
cell type: Differentiated C2C12 myotube
treatment: Untreated
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| Treatment protocol |
Myotubes were either untreated or treated with 10mM ammonium acetate for 3 or 24 hours (n=3 biological replicates)
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| Growth protocol |
10% fetal bovine serum in Dulbecco’s modified Eagle’s medium [DMEM] with 10% fetal calf serum until 80% confluence, replaced by 2% horse serum DMEM for 48 hours of differentiation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were pelleted and frozen at -80 degrees C. The Omni-ATAC protocol for cells was used for extraction and library preparation as described in Corces et al., 2017 without modifications. PMID: 28846090
ATACseq libraries were prepared at the UM Epigenomics Core by using the Omni-ATAC protocol for cells as described in Corces at al., 2017 without modifications. PMID: 28846090
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Sequencing and analysis were performed at the University of Michigan according to their pipeline. In brief, Snakemake was used to manage the bioinformatics workflow. FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of each sample.
TrimGalore (https://github.com/FelixKrueger/TrimGalore) (v0.4.5) and Cutadapt(v1.15) were applied using the following parameters: --nextera -e 0.1 –stringency 6 –length 20 –nextseq 20.
Trimmed reads were aligned to mm10 with Bowtie2 (v2.3.4.1) with the following parameters: -X 2000 –no-mixed –no-discordant, and defaults multi-seed length of 20bp with 0 mismatches. Duplicate reads were marked with Picard (http://broadinstitute.github.io/picard/) (v2.20.2). Alignments to autosomes were retained (while sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard were removed, and alignments below a MAPQ threshold were removed. These filtering steps were performed with SAMtools(30) (v1.2) and the flags: -q 10 -F 1024. Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) were removed with bedtools(31) (v2.28.0).
Sample-wise peaks were called with macs2(32) (v2.1.2) with flags: -f BAM –nomodel –shift -100 –extsize 200 –gsize mm. Peaks over all samples are then merged with bedops(33) (v2.4.36). MultiQC(34) (v1.7) generated a report combining FastQC, trimming, alignment, and duplicate calling over all the samples. For ATAC-specific QC metrics, ataqv (Ataqv)(35) was used (v1.0.0).
For each model and contrast, edgeR Bioconductor package(36) (v3.26.8) was used to identify regions of DAC. For each sample, the number of reads in the merged peaks is counted for each sample, and a library size normalization factor is determined. The common, trended, and tagwise negative binomial dispersions of replicates are calculated. Each model is fit using the glmQLFit function, and each contrast tested with an empirical Bayes quasi-likelihood F-test. The DAC are then annotated to genic and CpG island annotations using the annotatr Bioconductor package(37) (v1.10.0).
Genome_build: mm10
Supplementary_files_format_and_content: Excel, differential expression comparisons with each treatment group including annotated and non-annotated chromatin regions
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| Submission date |
Apr 07, 2021 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Srinivasan Dasarathy |
| E-mail(s) |
dasaras@ccf.org
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| Phone |
216-318-7010
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| Organization name |
Cleveland Clinic Lerner Research Institute
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| Department |
Inflammation and Immunity
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| Lab |
Dasarathy Lab
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| Street address |
9500 Euclid Ave
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| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE171642 |
Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia [ATAC-seq] |
| GSE171645 |
Integrated molecular landscape perturbations underlie cellular responses during hyperammonemia |
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| Relations |
| BioSample |
SAMN18648934 |
| SRA |
SRX10532480 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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