|
| Status |
Public on Sep 14, 2022 |
| Title |
WID2V_0006_L |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/C
age (weeks): 9
tratment: Vehicule
|
| Treatment protocol |
The 3 infected groups were given vehicle, Tet1 (at 40 mpkd) or Tet2 (at 1 mpkd) by daily intraperitoneal injection (mock group respectively injected with vehicule as well).
|
| Growth protocol |
We subjected 8 week-old female BALB/cN mice to either mock or intranasal inoculation with 175 PFU of the IFV H1N1 PR8 strain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen) and then extracted and cleaned using Direct-zol-96 RNA kit (Zymo Research). 1 ug of total RNA was used for the construction of sequencing libraries.
Transcriptome Library construction Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
Influenza H1N1 PR8 H1N1 PR8 virus infected
|
| Data processing |
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles FASTA_FILE.fa --sjdbGTFfile GTF_FILE.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
The RUV R package was used to remove batch effects.
A threshold of 1 log2 absolute fold change and p-value larger than 0.05 were considered when identifying the differentially expressed genes.
The clusterProfiler (version 3.10.1) package was then used to perform various Enrichment Analysis on the obtained results.
Genome_build: rnm10
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)
|
| |
|
| Submission date |
May 09, 2021 |
| Last update date |
Sep 14, 2022 |
| Contact name |
Gaby El Alam |
| E-mail(s) |
gaby.elalam@epfl.ch
|
| Organization name |
École polytechnique fédérale de Lausanne
|
| Department |
SV LISP
|
| Lab |
Laboratory of Integrative Systems Physiology
|
| Street address |
Station 15
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE174124 |
Tetracycline-induced mitohormesis mediates disease tolerance against influenza |
|
| Relations |
| BioSample |
SAMN19081096 |
| SRA |
SRX10823689 |
