|
| Status |
Public on Apr 09, 2021 |
| Title |
02-P005175-S022-R01: cellbender counts |
| Sample type |
SRA |
| |
|
| Source name |
COVID-19 autpsy tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
disease state: COVID-19
sampleID: 02-P005175-S022-R01
donor: D1
processing: nuclei
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dissociated individual cells or isolated individual nuclei from fresh, frozen, or cryopreserved COVID-19 autopsy samples; bulk samples were lysed in RLT buffer + 1% beta mercaptoethanol
3' RNAseq (10x kit V3 chemistry) for sc/snRNA-seq; Smart-seq2 for bulk RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Cellbender remove-background corrected single-cell or single nucleus RNA-Seq (10X) Cellranger counts, stored as an HDF5 file.
|
| Data processing |
sc/snRNA-seq: 3' RNAseq (10x kit V3 chemistry)
sc/snRNA-seq: Demultiplexing is run using Cell Ranger mkfastq.
sc/snRNA-seq: Counts matrix is generated using the Cumulus cellranger_workflow in Terra.
sc/snRNA-seq: Ambient RNA is removed using Cellbender remove-background workflow in Terra.
bulk RNA-seq: Demultiplexing is run using bcl2fastq
bulk RNA-seq: Alignment peformed using STAR
bulk RNA-seq: Counts matrix generated using RSEM
Supplementary_files_format_and_content: Raw count or cellbender count matrices are in the HDF5 Feature Barcode Matrix Format used by 10x, bulk counts matrices are provided as an RSEM counts matrix, and metadata files are comma-delimited text.
|
| |
|
| Submission date |
Apr 08, 2021 |
| Last update date |
Apr 09, 2021 |
| Contact name |
Caroline Porter |
| Organization name |
Broad Institute
|
| Department |
Klarman Cell Observatory
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL27644 |
| Series (1) |
| GSE171668 |
COVID-19 tissue atlases reveal SARS-COV-2 pathology and cellular targets |
|
| Relations |
| BioSample |
SAMN18653526 |
