|
| Status |
Public on Mar 03, 2021 |
| Title |
1172: COMET_1172_CD45_Day5 |
| Sample type |
SRA |
| |
|
| Source name |
Tracheal Aspirate
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 1172
disease state: COVID-19 ARDS
age: 51
gender: M
race: Other
hispanic ethnicity: Y
30 day mortality: N
development of vap: Y
lrti pathogen: Citrobacter koserii
reason for intubation: COVID-19 ARDS
sample obtained days before vap: 5
sample obtained days since intubation: 5
tissue: Tracheal Aspirate
|
| Treatment protocol |
TA was freshly processed in a BSL-3, dissociated in collagenase type 4 and DnaseI, filtered, and cells washed and purified for CD45 using MojoSort (Biolegend)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell suspension was counted and loaded onto a 10X Genomics Chip A aiming to caputre 10,000 cells (10X Genomics).
10X Genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
single cell RNA sequencing
*** Raw data is not included in this GEO submission due to patient privacy concerns ***
|
| Data processing |
alignment using STAR aligner to a custom genome containing GRCh38 and SARS2 isolate Wuhan-Hu-1
Genome_build: mm9
Supplementary_files_format_and_content: Readcount matrices generated through 10X genomics cellranger pipeline v3.0
|
| |
|
| Submission date |
Mar 02, 2021 |
| Last update date |
Jul 12, 2024 |
| Contact name |
Beth Shoshana Zha |
| E-mail(s) |
shoshana.zha@ucsf.edu
|
| Organization name |
University of California San Francisco
|
| Department |
Medicine
|
| Street address |
400 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL27644 |
| Series (2) |
| GSE168018 |
Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 (scRNA-seq) |
| GSE168019 |
Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 |
|
| Relations |
| BioSample |
SAMN18105629 |
