|
| Status |
Public on Jan 27, 2024 |
| Title |
Muscle_Regen_Injured_48hours_replicate1 |
| 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 |
SAMN39621554 |
| SRA |
SRX23409655 |
