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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 11, 2022 |
| Title |
1hpi, ATAC Rep1 |
| Sample type |
SRA |
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| Source name |
1 hour post-injured satellite cells followed by in situ fixation
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Skeletal muscle
cell type: Muscle stem cells
treatment: BaCl2 injury
time: 1hpi
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| Treatment protocol |
Mouse hind limb was injured by BaCl2 injection. Mice were perfused with PFA before satellite cell isolation.
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| Growth protocol |
N/A
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| 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
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| 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.
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| Submission date |
Nov 17, 2021 |
| Last update date |
Aug 11, 2022 |
| Contact name |
Tom Cheung |
| Organization name |
Hong Kong University of Science and Technology
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| Department |
Division of Life Science
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| Street address |
Clear Water Bay, Kowloon
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| City |
Hong Kong |
| ZIP/Postal code |
N/A |
| Country |
Hong Kong |
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| 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 |
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| Relations |
| BioSample |
SAMN23243588 |
| SRA |
SRX13158628 |
| 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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