|
Status |
Public on Mar 27, 2023 |
Title |
BM4_BioRep3_scRNAseq |
Sample type |
SRA |
|
|
Source name |
Bone marrow
|
Organism |
Homo sapiens |
Characteristics |
tissue: Bone marrow Sex: Male age: 75 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' v3.1 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
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|
|
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 |
SAMN33828615 |
SRA |
SRX19729003 |