|
| Status |
Public on Sep 20, 2018 |
| Title |
E2_destGFP_neg_4 |
| Sample type |
SRA |
| |
|
| Source name |
E2_destGFP_neg
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
mcherry-iav infection status: uninfected
gfp-iav infection status: destGFP-IAV infected
cell type: FACS-sorted cells from lung
gfp/dest fluorescence: negative
mcherry fluorescence level: negative
|
| Treatment protocol |
Mice were infected with 10^5 pfu of the indicated virus.
|
| Growth protocol |
Lungs from infefected C57BL/6 were taken at 24 hours post infection. Live CD45-CD31- cells were FACS sorted directly into cell lysis buffer for RNA extraction.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from FACS-sorted cells using RNeasy Micro or Micro Plus kit (Qiagen)
cDNA libraries were prepared using the SMARTer Universal Low Input RNA Kit (Takara Bio)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample11-1_S38
destGFP experiment (#2) ; destabilized GFP negative FACS-sorted cells from lung of mouse infected with destabilized GFP IAV
|
| Data processing |
Raw sequence reads were mapped to mouse genome and influenza (H1N1) transcripts separately using the Bowtie2 aligner (v2.2.4) with local mode, -L22 and -N 1 parameters.
Mapped read were sorted and filtered by removing PCR duplicates with Samtools (v1.16)
Expression was quantified using featureCounts from the Subread package (v1.5) with ENSEMBL gene models (GRCm38.87) for mouse expression and a custom annotation file (file provided with manuscript) for influenza expression.
Differentially expressed genes were determined using edgeR from the bioconductor package.
Genome_build: mm10 and influenza (H1N1) PR8mRNA-var
Supplementary_files_format_and_content: raw expression counts
|
| |
|
| Submission date |
Apr 06, 2018 |
| Last update date |
Sep 20, 2018 |
| Contact name |
Ryan Langlois |
| E-mail(s) |
langlois@umn.edu
|
| Phone |
6126253633
|
| Organization name |
University of Minnesota
|
| Street address |
689 23rd Ave SE, 1-117 MRF
|
| City |
MINNEAPOLIS |
| State/province |
MN |
| ZIP/Postal code |
55401 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE112794 |
Influenza virus replication intensity and round of infection dictates the cellular response in vivo |
|
| Relations |
| BioSample |
SAMN08874769 |
| SRA |
SRX3897328 |
