|
Status |
Public on Mar 03, 2021 |
Title |
1047: COMET_1047_CD45_Day2 |
Sample type |
SRA |
|
|
Source name |
Tracheal Aspirate
|
Organism |
Homo sapiens |
Characteristics |
patient id: 1047 disease state: COVID-19 ARDS age: 48 gender: F race: Other hispanic ethnicity: N 30 day mortality: Y development of vap: Y lrti pathogen: Methicillin susceptible Staphylococcus aureus reason for intubation: COVID-19 ARDS sample obtained days before vap: 16 sample obtained days since intubation: 9 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 |
SAMN18105682 |