|
| Status |
Public on Jun 01, 2016 |
| Title |
Sp_M_D28_8048x8026_77 |
| Sample type |
RNA |
| |
|
| Source name |
Spleen Tissue from Mock infected Line 8048x8026 at Day 28
|
| Organism |
Mus musculus |
| Characteristics |
Sex: male
tissue: Spleen
collaborative cross line (genetic background): 8048x8026
animal number (rxid): 77
treatmock infectedent: Mock infected
timepoint: Day 28
batch: 1
|
| 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 |
Age- and sex-matched eight to ten week old mice were subcutaneously inoculated in the rear footpad with 100 PFU WN-TX. 3 animals from each line and condition were humanely euthanized for necropsy and RNA from the spleen was isolated.
|
| 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 a Mice Gene expression data from a Mice Mock infected
|
| 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 both through standard RMA and oligomask. Both filtered and unfiltered outputs are included in this submission.
|
| |
|
| Submission date |
May 31, 2016 |
| Last update date |
Jun 01, 2016 |
| 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) |
| GSE82046 |
A Mouse Model of Chronic West Nile Virus Infection |
|
