|
| Status |
Public on Jan 27, 2024 |
| Title |
Muscle_NoInjury_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Skeletal Muscle Hindlimb
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Skeletal Muscle Hindlimb
cell line: Tissue disection, Collagenase 2/Dispase digestion. Immune Cell Depleted
cell type: All Muscle tissue cells
genotype: C57BL6 mice wt
treatment: Collagenase digestion of tissue
|
| Treatment protocol |
Treated with 1.2% barium chloride (wt/vol in H2O)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Dissected tissue, snap frozen, homogenized with gentleMACS
Chromium Next GEM Single-Cell 3ʹ Reagent Kits v3.1 (10× Gemomis, CG000204)with size selection using SPRI beads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10X Chromium Next GEM Single Cell 3ʹ v3.1
|
| Data processing |
Filtering of high-quality cells and creation of the Cell-gene matrix was done using CellRanger v6.0.1 (scRNAseq)
Creation of the seurat objects and other down-stream analyses were done using Seurat Version 4.0.0
The raw gene expression counts for all cells were SCT transformed with regression of mitochondrial gene expression, but MuSCs were log-normalized and scaled.
Assembly: mm10
Supplementary files format and content: rds file of seurat object (in R) containingraw gene expression matrix, dimensionality reduction matrices, 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 |
GPL19057 |
| Series (1) |
| GSE199499 |
Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state |
|
| Relations |
| BioSample |
SAMN39621548 |
| SRA |
SRX23409661 |
