|
| Status |
Public on Jun 21, 2022 |
| Title |
W1_WT_flu |
| Sample type |
SRA |
| |
|
| Source name |
wild type_flu-infected_NK cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype/variation: wild type
treatment: flu-infected
cell type: purified splenic NK cells
|
| Treatment protocol |
Mice were intranasally infected with 50 PFU of PR8 H1N1 influenza A virus (IAV). At 5 days post-infection, animals were sacrificed and their spleens extracted.
|
| Growth protocol |
Six to ten-week old C57BL/6J mice were bred at the RI-MUHC, Montreal, QC, Canada. Experiment were performed age- and sex-matched mice and all animal studies were conducted in accordance with the guidelines of and approved by the Animal Research Ethics Board of McGill University (project ID: 5860).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Splenocytes were harvested and pure pan-NK cells were isolated using the EasySep Mouse NK Cell Isolation Kit (StemCell). Cell purity was then ascertained by flow cytometry and cells were lysed and prepped for RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
bulk RNA library
JD-MD_W1_NEY922A14-16_S8
|
| Data processing |
Fastqs were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode (-q 20 --phred33)
Reads were pseudoaligned to mm10 using kallisto's quant function (Bray et al.) in paired-end mode
Quantification estimates were obtained from abundance.h5 files using the R package tximport (Soneson et al.)
Genome_build: mm10.81
Supplementary_files_format_and_content: Mus_musculus.mm10.81.kallisto.gene_level.raw_counts.txt includes raw count values for each sample; Mus_musculus.mm10.81.kallisto.gene_level.lengthScaledTPM_counts.txt includes counts from abundance estimates scaled using the average transcript length across samples and the library size
|
| |
|
| Submission date |
Dec 15, 2020 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Luis B Barreiro |
| E-mail(s) |
barreirolabchicago@gmail.com
|
| Organization name |
University of Chicago
|
| Lab |
Barreiro Lab
|
| Street address |
900 E 57th Street
|
| City |
Chicago |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE163290 |
Cyclophilin D promotes disease tolerance to influenza A virus infection by licensing NK cell development and function |
|
| Relations |
| BioSample |
SAMN17087372 |
| SRA |
SRX9688706 |
