|
| Status |
Public on Mar 08, 2022 |
| Title |
siNTC-1_IAV |
| Sample type |
SRA |
| |
|
| Source name |
A549 (CCL-185)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: adenocarcinomic human alveolar basal epithelial cells
sirna: siNTC
agent: influenza A virus
|
| Treatment protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted using Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations.
Poly-A plus RNA was enriched from ~0.1 ug of total RNA and used to generate libraries using the Illumina TruSeq kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Non-targeting control (Infected)
|
| Data processing |
Base calling was using Illumina's bcl2fastq2-v2.17.1 converter
A genome index was built with STAR (v2.5.1b) using the human hg38 genome .
Reads were aligned to the hg38 reference using the STAR software version 2.5.1b with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR.
Differential gene expression was analyzed with the R (version 3.3.1) software DESeq2 (version 1.12.1)
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited table of raw read counts per gene
|
| |
|
| Submission date |
Mar 04, 2021 |
| Last update date |
Mar 08, 2022 |
| Contact name |
Adam Hage |
| Organization name |
University of Texas Medical Branch at Galveston
|
| Department |
Microbiology and Immunology
|
| Lab |
Rajsbaum Lab
|
| Street address |
301 University Blvd
|
| City |
Galveston |
| State/province |
Texas |
| ZIP/Postal code |
77555 |
| Country |
USA |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE168255 |
The RNA Helicase DHX16 Provides Specific Viral RNA for RIG-I to Trigger Innate Antiviral Immunity |
|
| Relations |
| BioSample |
SAMN18140343 |
| SRA |
SRX10239437 |
