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Sample GSM7230029 Query DataSets for GSM7230029
Status Public on May 06, 2024
Title 02 Nedd4L-WT 5000 freshly isolated muscle stem cells
Sample type SRA
Source name Skeletal muscle
Organism Mus musculus
Characteristics tissue: Skeletal muscle
cell type: Muscle stem cell
genotype: Nedd4L-WT
Extracted molecule genomic DNA
Extraction protocol Cells were sorted into ATAC-Seq Lysis buffer(10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin) and then washed in a wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). After, the cells were centrifuged at 800g and DNA tagementation could be performed using the transposition mixture (5 μl of Tagment DNA (TD) buffer, 3.2 μl PBS, 0.89 μl Tn5, 0.1% Tween-20, 0.01% Digitonin and 0.75 μl water) for 20 minutes at 37oC.
Sequencing ready libaries were prepared by incorporating Illumina adaptors with PCR and then purifying and size selecting the DNA using AMPure beads
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Data processing Adapters were removed from raw ATAC-seq reads using Trimmomatic (version 0.39, parameters: LEADING:10 TRAILING:10 MINLEN:50).
Paired reads were aligned to mm10 using BWA-MEM (version 0.7.17).
Samtools was used to index and filter (version 1.16.1, mapping quality > 30).
Duplicated reads were removed using Picard (version 2.26.3).
ATAC-seq peaks were called with MACS2 (version, parameters: --nomodel --shift -100 --extsize 200 –broad, --gsize mm).
Assembly: mm10
Supplementary files format and content: tab-delimited text files describing the Broad and gapped peak (*_peaks.broadPeak, *_peaks.gappedPeak, and *_peaks.xls).
Submission date Apr 26, 2023
Last update date May 06, 2024
Contact name Vahab Soleimani
Organization name McGill University
Department Human Genetics
Street address 3640 rue University
City Montreal
State/province QC
ZIP/Postal code H3A 0C7
Country Canada
Platform ID GPL24247
Series (2)
GSE230620 ATAC-Seq of WT and Nedd4L-cKO Muscle stem cells
GSE230622 The E3 Ubiquitin Ligase Nedd4L Acts as a Checkpoint Against Activation in Quiescent Muscle Stem Cells
BioSample SAMN34384242
SRA SRX20109666

Supplementary file Size Download File type/resource
GSM7230029_N4LWT04_SOL1639A3-1_S3_L001_peaks.broadPeak.gz 1.7 Mb (ftp)(http) BROADPEAK
GSM7230029_N4LWT04_SOL1639A3-1_S3_L001_peaks.gappedPeak.gz 2.5 Mb (ftp)(http) GAPPEDPEAK
GSM7230029_N4LWT04_SOL1639A3-1_S3_L001_peaks.txt.gz 2.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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