|
| Status |
Public on Jan 03, 2017 |
| Title |
Sp_W_D12_16680x8016_m47 |
| Sample type |
RNA |
| |
|
| Source name |
Spleen Tissue from West Nile Virus infected Line 16680x8016 at Day 12 post infection
|
| Organism |
Mus musculus |
| Characteristics |
batch: 2
Sex: m
tissue: Spleen
collaborative cross line (genetic background): 16680x8016
animal number (rxid): m47
treatment: West Nile Virus infected
days post-infection: 12
collaborative cross line (genetic background, unc_id): CC(055x028)/F1
|
| Treatment protocol |
Per the manufacturer's protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation overnight, tissue was removed from RNAlater and stored at -80°C until RNA isolation in TRIzol or RLT buffer.
|
| Growth protocol |
spleen was isolated for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleen tissues were thawed, transferred to lysis buffer either TRIzol (Life Technologies) or RLT Reagent (Qiagen Inc.) and homogenized. RNA was isolated using Qiagen miRNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip.
|
| Label |
biotin
|
| Label protocol |
RNA samples were prepared for whole transcriptome expression analysis using the WT PLUS Reagent Kit following the manufacturer’s recommended protocol (Affymetrix, Inc. Santa Clara, CA). 100 ng of total RNA was used to prepare the hybridization ready targets.
|
| |
|
| Hybridization protocol |
Individual sense-strand DNA targets were hybridized to Mouse Gene 2.1 ST 24-Array Plates (Affymetrix, Inc.) using the GeneTitan Multi-Channel (MC) Instrument for hybridization, array staining and washing and scanning. Quality Control Metrics for Hybridization, Labeling and Sample quality were generated using the Affymetrix Expression Console software. All samples passed the QC criteria.
|
| Scan protocol |
Affy arrays were scanned with an Affymetrix GeneTitan
|
| Description |
Gene expression data from West Nile Virus infected Mice at Day 12 post infection
|
| Data processing |
Data was analyzed using R(3.01) and oligo and limma packages. Matrix was generated use RMA. Samples were background corrected and quantile normalized
|
| |
|
| Submission date |
Dec 07, 2016 |
| Last update date |
Jan 03, 2017 |
| 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 |
GPL17400 |
| Series (1) |
| GSE91003 |
Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross |
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