|
| Status |
Public on Dec 14, 2018 |
| Title |
KO WNV 12h rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
time: 12h
treatment: WNV infection
genotype: Irf5-/-
replicate: 3
|
| Treatment protocol |
BMDCs were resuspended in serum-free RPMI with 2.5 MOI of WNV for 1.5 hours with gentle rocking.
|
| Growth protocol |
BMDCs were cultured in complete RPMI supplemented with recombinant mouse IL-4 (40ng/ml, Invivogen) and GM-CSF (40ng/ml, Invivogen) for 7-9 days, changing media on day 3. Cells were kept at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy mini kit (QIAGEN) with on-column DNase treatment.
KAPA stranded RNA-seq kit with Ribo Erase
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.0)
Genome_build: mouse genome (mm10)
Supplementary_files_format_and_content: We mapped reads to the mouse reference genome (mm10) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq. HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed. After counst were generated we normalized with voom from the limma package in R.
|
| |
|
| Submission date |
May 29, 2018 |
| Last update date |
Dec 14, 2018 |
| Contact name |
Michael Gale, Jr |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Washington
|
| Department |
Immunology
|
| Street address |
750 Republican St. E360, Box 358059
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE114992 |
IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection (RNA-Seq) |
| GSE114993 |
IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection |
|
| Relations |
| BioSample |
SAMN09273978 |
| SRA |
SRX4133948 |
