|
| Status |
Public on Mar 05, 2021 |
| Title |
P9151-3 |
| Sample type |
SRA |
| |
|
| Source name |
Bronchial brushing
|
| Organism |
Homo sapiens |
| Characteristics |
covid-19: Positive
patient id: 9151
tissue/sample type: Bronchial brushing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
https://www.protocols.io/view/cell-dissociation-from-nasal-and-bronchial-brushin-qubdwsn
Libraries were prepared with 10x Genomics 5' gene expression (GEX) reagents according to the manufacturer protocol (CG000086_RevM).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were demultiplexed using with cellranger mkfastq command (v3.1.0). Reads were aligned to a custom built genome (human GRCh38.93 and SARS-CoV-2 NC_045512.2) and counted by gene by cell with cellranger count command (v3.1.0), producing raw and filtered gene expression matrices.
Genome_build: custom (human GRCh38.93 and SARS-CoV-2 NC_045512.2)
Supplementary_files_format_and_content: gene expression count matrices
|
| |
|
| Submission date |
Mar 04, 2021 |
| Last update date |
Mar 05, 2021 |
| Contact name |
Alexander V Misharin |
| E-mail(s) |
a-misharin@northwestern.edu
|
| Organization name |
Northwestern University
|
| Street address |
303 E Superior
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL27644 |
| Series (1) |
| GSE168215 |
Single cell RNA-seq analysis of bronchial epithelium in patients with severe SARS-CoV-2 pneumonia |
|
| Relations |
| BioSample |
SAMN18137987 |
