|
| Status |
Public on Oct 19, 2023 |
| Title |
Trx_20wk_Mut, rep 1, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Isolated Srcap mutant HSPCs
tissue: Bone marrow
strain: C57BL/6
age: 20 weeks post-transplantation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
20,000 donor (CD45.2) HSPCs in the bone marrow were isolated after competitive transplantation for 20 weeks. Each independent Sample were used as input for 10X platform droplet-based library construction.
Library was performed using 10x platform 3v31 assay using chromium Single Cell 3’ solution without multiplexing according to the manufacter’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Paired-end sequencing data were mapped and quantified using Cell Ranger Single Cell Suite v3.1.0 to the mouse genome (mm10) provided by 10x Genomics’ Cell Ranger.
Cell Ranger count files of each Sample were combined and normalized using Cell Ranger aggregate.
Cells with 6,500-30,000 detected genes and less than 10% total mitochondrial gene expression were filtered and retained for analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Apr 20, 2023 |
| Last update date |
Oct 19, 2023 |
| Contact name |
Margaret Goodell |
| E-mail(s) |
goodell@bcm.edu
|
| Phone |
7137921265
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor Plz, Rm N1030
|
| City |
HOUSTON |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE230153 |
SRCAP Mutations Drive Clonal Hematopoiesis Through Epigenetic and DNA Repair Dysregulation [scRNA-Seq] |
| GSE230155 |
SRCAP Mutations Drive Clonal Hematopoiesis Through Epigenetic and DNA Repair Dysregulation |
|
| Relations |
| BioSample |
SAMN34264336 |
| SRA |
SRX20021912 |
