|
| Status |
Public on Mar 03, 2023 |
| Title |
LSK scRNA |
| Sample type |
SRA |
| |
|
| Source name |
Lin-SCA1+KIT+ bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Primary bone marrow
genotype: Wild type
cell population: Lin-SCA1+KIT+
|
| Treatment protocol |
Bone marrow was collected from healthy controls and targeted population isolated by FACS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated and cDNA constructed using the 10x Genomics Single cell 3' Library and Gel Bead Kit according to the manufacturer's protocol.
Libraries were constructed using Chromium Single Cell 3’ library and Gel Bead Kits (10x Genomics) and sequencing performed on a HiSeq 2500 DNA Sequencer (with a 26 base read for cell and molecule barcodes, an 8 base library index read, and a 98 base insert read)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequencing data was processed using RTA (v1.18.64) and Casava (v1.8.2)
Sequencing data was demultiplexed and aligned to the the mm10 genome using the 10x Genomics Cell Ranger software (v2.0.0).
Count matrices were constructed using the Read10X function in Seurat (v2.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: UMI counts
|
| |
|
| Submission date |
Mar 04, 2021 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Dave M Bodine |
| Organization name |
National Institutes of Health
|
| Department |
National Human Genome Research Institute
|
| Street address |
49 Convent Drive, 4A19
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE168259 |
Identification and isolation of hematopoietic stem and progenitor cell populations (scRNA-seq) |
| GSE168260 |
Identification and isolation of hematopoietic stem and progenitor cell populations |
|
| Relations |
| BioSample |
SAMN18142670 |
| SRA |
SRX10240663 |
