|
| Status |
Public on Dec 14, 2018 |
| Title |
WNV 12h input |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
time: 12h
treatment: WNV infection
genotype: WT
|
| 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 |
genomic DNA |
| Extraction protocol |
Chromatin was isolated using a truChIP chromatin shearing kit (Covaris) and sheared using M220 focused-ultrasonicator (Covaris). Sheared chromatin was run on an agarose gel and band corresponding to size 200-700bp was extracted. Immunoprecipitation was performed with validated IRF5 antibodies (Bethyl A303-385 and 386).
Exonuclease processing of sheared chromatin and library construction was performed using ChIP-exo kit (Active Motif).
Library size and quality was assessed using High Sensitivity DNA kit (Agilent) on the 2100 Bioanalyzer (Agilent). Next-generation sequencing was performed on the Illumina HiSeq 2500 instrument by the Genome Technology Access Center (Washington University).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-exo
|
| Data processing |
Next-generation sequencing was performed on the Illumina HiSeq 2500 instrument by the Genome Technology Access Center (Washington University).
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 Bowtie v1.1.1
Genome_build: mouse genome (mm10)
Supplementary_files_format_and_content: We mapped reads to the mouse reference genome (mm10) from Illumina's igenomes using Bowtie v1.1.1. After mapping, we called peaks using GEM v3.1 on replicates together with corresponding input-ip samples as controls.
|
| |
|
| Submission date |
May 29, 2018 |
| Last update date |
Dec 14, 2018 |
| Contact name |
Michael Gale, Jr |
| E-mail(s) |
uw_galelab_geo@uw.edu
|
| 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 |
GPL17021 |
| Series (2) |
| GSE114991 |
IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection (ChIP-Seq) |
| GSE114993 |
IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection |
|
| Relations |
| BioSample |
SAMN09273943 |
| SRA |
SRX4133402 |
