|
| Status |
Public on Apr 01, 2024 |
| Title |
BM SLAM LSK HSPCs (multiome-snRNA) |
| Sample type |
SRA |
| |
|
| Source name |
SLAM LSK HSPCs isolated from BM of C57Bl/6 mice
|
| Organism |
Mus |
| Characteristics |
strain: C57Bl/6
time points: 2-4 months old mice
tissue: Bone marrow (BM)
cell type: SLAM LSK HSPCs
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Femurs and tibias were harvested from C57Bl/6 mice, flushed, crushed, filtered, and washed. Total BM cells were labeled and CD150+/CD48-/Lineage-/Sca-1+/c-Kit+/CD45+ HSPCs sorted and processed for 10X multiome analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
filtered_feature_bc_matrix.h5
|
| Data processing |
cellranger-arc-2.0.0 to process snRNAseq and scATACseq multiome
Assembly: refdata-cellranger-arc-mm10-2020-A-2.0.0
Supplementary files format and content: atac_fragments.tsv.gz (10x cellranger-arc ATACseq fragments file)
atac_fragments.tsv.gz.tbi (Tabix index of fragments interval )
filtered_feature_bc_matrix.h5 (Multiomimodal h5 object containing filtered gene expression and peak counts)
|
| |
|
| Submission date |
Jul 12, 2022 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Tomer Itkin |
| E-mail(s) |
toi2003@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Medicine
|
| Lab |
Rafii
|
| Street address |
1300 York Avenue, A-869
|
| City |
NY |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL31136 |
| Series (2) |
| GSE169431 |
Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing |
| GSE208039 |
Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [snRNA/ATACseq HSPC Multiome] |
|
| Relations |
| BioSample |
SAMN29660420 |
| SRA |
SRX16141507 |
