|
| Status |
Public on May 15, 2023 |
| Title |
RNA-seq dataset: PR8-infected IFNLR-/- mouse #5 |
| Sample type |
SRA |
| |
|
| Source name |
Whole lungs of PR8-infected IFNLR-/- mouse
|
| Organisms |
Mus musculus; Influenza A virus (A/Puerto Rico/8/1934(H1N1)) |
| Characteristics |
tissue: Lung
mouse strain: IFNLR-/-
treatment: PR8-only infection
|
| Treatment protocol |
Mice were intranashally inoculated with 1,000 TCID50 units of PR8 virus in 50µL PBS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole lungs were homogenized in QIAzol. The total RNA was extracted using miRNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen), followed by poly(A) mRNA enrichment.
The enriched poly(A) mRNAs were subject to RNA-seq library preparatin with NEBNext Ultra II RNA library prep kit for Illumina following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
FDK255_LP5
DIinfKOmice_mRNAseq_counts.txt
|
| Data processing |
For the RNA-seq dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the miRNA-seq dataset, miRNA primary quantification was performed in the GeneGlobe Data Analysis Center (Qiagen) for trimming, mapping, and unique molecular indices (UMI) analysis. Although both miRNAs and piRNAs were detected in the small RNA libraries, only miRNAs were used in the downstream analyses.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment.
Genome_build: GRCm38.99 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1) were used for RNA-seq
Supplementary_files_format_and_content: For the RNA-seq and miRNA-seq datasets, a tab-delimited text file containing the raw gene or miRNA counts for all the samples was provided.
|
| |
|
| Submission date |
Nov 04, 2021 |
| Last update date |
May 15, 2023 |
| Contact name |
Matthew Chung |
| E-mail(s) |
matt.chung@nih.gov
|
| Organization name |
NIAID (National Institute of Allergy and Infectious Diseases)
|
| Street address |
50 South Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL30928 |
| Series (1) |
| GSE188122 |
Influenza defective interfering virus promotes multiciliated cell differentiation and reduces the inflammatory response in mice |
|
| Relations |
| BioSample |
SAMN22882526 |
| SRA |
SRX12970152 |
