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Sample GSM8037550 Query DataSets for GSM8037550
Status Public on Jan 27, 2024
Title Muscle_Regen_Injured_48hours_replicate2
Sample type SRA
 
Source name Skeletal Muscle Hindlimb
Organism Mus musculus
Characteristics tissue: Skeletal Muscle Hindlimb
cell line: Dissected tissue, snap frozen, homogenized with gentleMACS
cell type: All Muscle cells
genotype: C57BL6 mice wt
treatment: BaCl2-treated muscle, snap frozen on dry ice
Treatment protocol Treated with 1.2% barium chloride (wt/vol in H2O)
Extracted molecule genomic DNA
Extraction protocol Dissected tissue, snap frozen, homogenized with gentleMACS
Tn5 insertion with combinatorial Indexing by serial barcode ligation, and size selection
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model BGISEQ-500
 
Description Library prep: Tn5 insertion with combinatorial Indexing and size selection
Data processing Demultiplexing of cells using an in-house python script, creation of fragment files using Snaptools v1.1
Creation of arrow files and further downstream analyses using ArchR Version 1.0.1 with mostly default parameters
For Arrow files, changed parameters include TSS enrichment cut off of 8 and unique fragment cutoff of 1000 was used.
Assembly: mm10
Supplementary files format and content: Arrow files (in R) containing accessibility matrix and other cell-type-related metadata.
 
Submission date Jan 26, 2024
Last update date Jan 30, 2024
Contact name Yarui Diao
E-mail(s) yarui.diao@duke.edu
Phone 9196847090
Organization name Duke University School of Medicine
Department Cell Biology
Lab Diao Lab
Street address 307 Research Drive, Box 3709
City Durham
State/province North Carolina
ZIP/Postal code 27710
Country USA
 
Platform ID GPL23479
Series (1)
GSE199499 Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state
Relations
BioSample SAMN39621553
SRA SRX23409656

Supplementary file Size Download File type/resource
GSM8037550_Injured_48hRep2.arrow 768.4 Mb (ftp)(http) ARROW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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