|
| Status |
Public on Mar 27, 2023 |
| Title |
BM2_BioRep2_scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow
Sex: Female
age: 37
disease state: HealthyDonor
bone marrow_involvement: NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was extracted and hybridized to polyT oligos on 10x Genomics or Seq-Well beads.
10x Genomics 3' v3 or v3.1, or Seq-Well S3 library construction methods were used to construct single-cell RNA-sequencing libraries. From the full-length cDNA, XV-seq was used to enrich and sequence mutation sites of interest (similar to Genotyping of Transcriptomes, GoT).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics 3' v3
BM_counts.tsv
BM_norm.tsv
BM_metadata.tsv
|
| Data processing |
For demultiplexing, we used cellranger-7.0.0 mkfastq or bcl2fastq v2.20.0.422, with identical results.
For alignment of scRNA-seq data and to generate gene expression matrices, we used cellranger-7.0.0 count.
For the analysis of XV-seq data, we used IronThrone-GoT.
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated transcript counts per cell
Supplementary files format and content: norm.tsv: tab-separated normalized transcript counts per cell
Supplementary files format and content: metadata.tsv: tab-separated metadata per cell
Supplementary files format and content: FilteredCells.txt: tab-separated number of UMIs with wildtype or mutant genotyping calls per cell
|
| |
|
| Submission date |
Mar 20, 2023 |
| Last update date |
Mar 27, 2023 |
| Contact name |
Peter van Galen |
| E-mail(s) |
petervangalen@gmail.com, pvangalen@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital / Broad Institute of MIT and Harvard
|
| Department |
Hematology
|
| Lab |
Van Galen Lab
|
| Street address |
4 Blackfan Circle
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE227690 |
Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin |
|
| Relations |
| BioSample |
SAMN33828621 |
| SRA |
SRX19728997 |
