|
| Status |
Public on Dec 14, 2018 |
| Title |
BMM WT mock 12h rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
BMM WT mock 12h
|
| Organism |
Mus musculus |
| Characteristics |
time: 12h
infection: Mock
genotype: WT
cell type: Bone marrow macrophages
replicate: 1
|
| Treatment protocol |
BMMs were resuspended in serum-free RPMI with 2.5 MOI of WNV for 1.5 hours with gentle rocking.
|
| Growth protocol |
BMMs were cultured in complete DMEM supplemented with recombinant mouse M-CSF (40ng/ml, Peprotech) for 7 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.
TruSeq RNA Library Prep Kit v2
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 HiSeq 2500 |
| |
|
| Description |
MacWT1-mock-12_S343_L008
|
| Data processing |
Constructed libraries were sequenced on an HiSeq 2500 Illumina platform, producing 50-nt single-end reads. 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)
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 counts were generated we normalized with voom from the limma package in R.
Genome_build: mouse genome (mm10)
Supplementary_files_format_and_content: raw count matrix
|
| |
|
| Submission date |
Aug 13, 2018 |
| Last update date |
Dec 14, 2018 |
| Contact name |
Michael Gale, Jr |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Minnesota
|
| Department |
Microbiology and Immunology
|
| Street address |
689 23rd Ave SE
|
| City |
Minneapolis |
| State/province |
Minnesota |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE114993 |
IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection |
| GSE118452 |
IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection (BMM_RNA-Seq) |
|
| Relations |
| BioSample |
SAMN09812780 |
| SRA |
SRX4548315 |
