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| Status |
Public on Apr 02, 2024 |
| Title |
Single cell multiome 10x from lineage-Sca1+ckit+ sorted marrow T58A cells replicate 2 ATAC |
| Sample type |
SRA |
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| Source name |
Lin-Scai+ckit+ marrow Cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Lin-Scai+ckit+ marrow Cells
genotype: T58A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single celll multiome analysis ( scRNA-Seq and scATAC-Seq) was done using nuclei isolated according to the manufacturers specifications (10X Genomics). For this, cells were sorted on a flow cytometer (Lin-Sca1+ckit+), and nuclei were prepared in buffer containing digitonin. Cells were counted, barcoded, and extraction was carried out in the Fred Hutch Cancer Center genomics core as described for the 10X genomics system.
After barcoding and extraction, single cell multiome libraries were constructed in the Fred Hutch Cancer Center genomics core using the 10X Genomics system. RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 kit. For CUT&RUN, cells were processed on a previously published, automated system at the Fred Hutch Cancer Center that uses KAPA DNA polymerase method for library preparation optimized for recovery of small DNA fragments.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
For single cell multiome, alignment was carried out using Cellranger-Arc from 10X genomics.
Data was analyzed using Seurat and Signac R packages. High quality cells were filtered for RNA (1,000 < reads < 25, 000) and DNA content (>70,000), and datasets were integrated and clustered to define cell categories.
Assembly: mm10
Supplementary files format and content: For single cell multiome data, gene expression values are provided as a matrix for each cell.
Library strategy: sc-multiome
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| Submission date |
Nov 14, 2023 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Brian Freie |
| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Basic Sciences
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| Street address |
1100 Fairview Ave N
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL30172 |
| Series (2) |
| GSE247756 |
RNASeq, multiome, and genomic profiling of hematopoietic progenitors and B cells from mice with a point mutation in MYC [Multiome] |
| GSE247757 |
A Germline Point Mutation in the MYC-FBW7 Phosphodegron Results in a Tumor-Prone Phenotype |
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| Relations |
| BioSample |
SAMN38256730 |
| SRA |
SRX22526611 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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