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Sample GSM5693761 Query DataSets for GSM5693761
Status Public on Aug 11, 2022
Title 32hpi, ATAC Rep2
Sample type SRA
 
Source name 32 hours post-injured satellite cells followed by in situ fixation
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Skeletal muscle
cell type: Muscle stem cells
treatment: BaCl2 injury
time: 32hpi
Treatment protocol Mouse hind limb was injured by BaCl2 injection. Mice were perfused with PFA before satellite cell isolation.
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol Isolated satellite cells were lysed using ATAC-seq lysis buffer ( (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Library was constructed based on protocols from Buenrostro et al., (2015) and Chen et al., (2016). Briefly, lysates were tagmented with Tn5 (Vazyme), reverse-crosslinked, and amplified using NEBNext High-Fidelity 2 x PCR Master Mix (NEB). Library was then sequenced using DNBSEQ-G400 sequencer (BGI).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model DNBSEQ-G400
 
Data processing Adapters were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters‘PE CROP: 50.
Trimmed reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with parameters ‘--minins 30 --maxins 2000 --dovetail -k 4 --very-sensitive-local’
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings.
Next, unmapped reads, duplicate reads, non-primary alignments, reads with their mate unmapped and read alignments with a mapping quality below 30 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1804 -f 2 -q 30 -b’.
Peak calling was performed on each individual replicate from the previous section using Genrich (v0.6, available at https://github.com/jsh58/Genrich) with the following parameters: -j -y -r -e chrM -v -f.
Genome_build: mm10
Supplementary_files_format_and_content: NarrowPeak files with blacklisted peaks removed; BigWig files of ATAC-seq signal along mm10 after downsampling step.
 
Submission date Nov 17, 2021
Last update date Aug 11, 2022
Contact name Tom Cheung
Organization name Hong Kong University of Science and Technology
Department Division of Life Science
Street address Clear Water Bay, Kowloon
City Hong Kong
ZIP/Postal code N/A
Country Hong Kong
 
Platform ID GPL28457
Series (2)
GSE189044 Chromatin structure profiling of mouse muscle stem cells by ATAC-seq
GSE189074 Comprehensive Analysis of Chromatin Accessibility Changes during Muscle Stem Cell Quiescence Exit and Self-renewal
Relations
BioSample SAMN23243599
SRA SRX13158639

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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