|
Status |
Public on Mar 03, 2021 |
Title |
1047: RR100e_00077 |
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 development of vap: Y study group: VAP - longitudinal sample obtained days before vap: 16 sample obtained days since intubation: 9 tissue: Tracheal Aspirate
|
Treatment protocol |
TA was collected and mixed 1:1 with DNA/RNA shield
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted with Zymo Pathogen Magbead Kit, treated with DNAse, and ribodeplted with FastSelect NEBNext Ultra II RNAseq Kit
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
bulk RNA sequencing *** Raw data is not included in this GEO submission due to patient privacy concerns ***
|
Data processing |
Pseudoalignment with kallisto 0.46.1 Genome_build: ENSEMBL v.99 Supplementary_files_format_and_content: Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport30, with the scaledTPM method.
|
|
|
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) |
GSE168017 |
Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 (bulkRNA-seq) |
GSE168019 |
Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 |
|
Relations |
BioSample |
SAMN18105611 |