|
| Status |
Public on Mar 03, 2021 |
| Title |
1154: RR100e_00304 |
| Sample type |
SRA |
| |
|
| Source name |
Tracheal Aspirate
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 1154
disease state: COVID-19 ARDS
age: 53
gender: M
race: Other
hispanic ethnicity: Y
development of vap: Y
study group: VAP - longitudinal
sample obtained days before vap: 14
sample obtained days since intubation: 6
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 |
SAMN18105558 |
