|
| Status |
Public on Jan 08, 2025 |
| Title |
2_young_mitoDendra2_High_ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: Mitochondria high HSCs
genotype: mitoDendra2 mice
age: young
|
| Treatment protocol |
Slam HSCs (CD150+CD48- LSK cells) were sorted and then pooled from CD117+ cells-enriched bone marrow cells of 8 young (7 to 17 weeks old) and 2 aged (70 weeks old) male mito-Dendra2 mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single nuclei of sorted HSCs were prepared according to the manufacturer's instruction.
Multiome single-cell/nuclei analysis was performed on the 10X Genomics platform using the Chromium Controller and the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics) following the manufacturer's instruction.
Single cell multiome analysis (single cell RNA-Seq and single cell ATAC-seq)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Raw unique molecular identifier (UMI)-based data files were mapped against the mm10 reference genome, and mapped reads were counted using the Cell Ranger ARC package (10x Genomics) with default parameters.
The Seurat package in R was used to analyze the scRNA-seq data, and the Signac package was used to analyze the scATAC-seq data.
To mitigate the effects of cell cycle heterogeneity, cell-cycle scoring and regression were performed using vars.to.regress of SCTransform. scRNA-seq and scATAC-seq data were integrated by weighted-nearest neighbor (WNN) analysis using FindMultiModalNeighbors.
Clusters were detected using FindClusters, and annotated based on feature genes.
Differentially expressed genes were identified by running FindAllMarkers or FindMarkers.
Assembly: mm10
Supplementary files format and content: An HDF5 file continaing a feature barcode matrix of scRNA-seq.
Supplementary files format and content: atac_peaks.bed containing locations of open-chromatin regions, atac_fragments.tsv.gz containing count and barcode information for every ATAC fragment, and per_barcode_metrics.csv containing ATAC and GEX read count summaries. These files can be loaded into R using Seurat and Signac.
|
| |
|
| Submission date |
Mar 29, 2024 |
| Last update date |
Jan 08, 2025 |
| Contact name |
Takayoshi Matsumura |
| Organization name |
National University of Singapore
|
| Street address |
14 Medical Drive #12-01
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE262784 |
Mitochondria-enriched hematopoietic stem cells exhibit elevated self-renewal capabilities, thriving within the context of aged bone marrow [single cell multiome] |
|
| Relations |
| BioSample |
SAMN40653360 |
| SRA |
SRX24098230 |
