|
| Status |
Public on Dec 08, 2021 |
| Title |
DOGMA-LLL_scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
technology: DOGMA-Seq - RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA and mitochondrial mRNA was extracted by hybridization to polyT oligos on Seq-Well or 10x beads. DNA for ATAC-seq was extracted using the 10x multiome protocol with adaptations as described in DOGMA-Seq (Mimitou et al., Nat Biotech 2021).
Seq-Well S3 and 10x 3' v3 single-cell RNA-sequencing library construction methods were utilized for mRNA libraries. MAESTER was used to enrich and sequence mitochondrial mRNA. The 10x Genomics multiome protocol was used for the multiome samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Demultiplexing using Illumina bcl2fastq2 v2.20.0
Alignment using STAR 2.7.2a or CellRanger version 3.1.0 or CellRanger-Arc
Generate single-cell expression matrix using custom scripts or CellRanger version 3.1.0 or CellRanger-Arc
MAESTER: generate single-cell variant call matrix using maegatk version 0.0.2
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrices, metadata, maegatk rds output with variant counts
|
| |
|
| Submission date |
Aug 24, 2021 |
| Last update date |
Dec 08, 2021 |
| 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) |
| GSE182685 |
Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations |
|
| Relations |
| BioSample |
SAMN20962073 |
| SRA |
SRX11896363 |
