|
| Status |
Public on May 01, 2014 |
| Title |
Liver Tissue of line 15156x1566 at Day 3_Mock Treated_196 |
| Sample type |
RNA |
| |
|
| Source name |
Collaborative Cross line 15156x1566 Mock Treated at D3 in Liver
|
| Organism |
Mus musculus |
| Characteristics |
Sex: m
tissue: Liver
treatment: Mock Treated
timepoint: Day 3
collaborative cross line (genetic background): 15156x1566
animal number (rxid): 196
age: 6-8 weeks
|
| 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 |
6-to-8 week old male mice from CC-RIX lines 13140x3015 or 15156x1566 were infected intraperitoneally with 100 FFU of MA-ZEBOV or equivalent volume of mock infection buffer. 3 animals from each line and condition were humanely euthanized for necropsy, and collection of liver and spleen were performed for RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver and 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 Mock treated
|
| Data processing |
Data was analyzed using R(3.01) and oligo and limma packages. Matrix was generated with RMA. Samples were background corrected and quantile normalized
|
| |
|
| Submission date |
Apr 30, 2014 |
| Last update date |
May 01, 2014 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Michael G. Katze, Ph.D
|
| Street address |
Rosen Building 960 Republican St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
| |
|
| Platform ID |
GPL17400 |
| Series (1) |
| GSE57214 |
Host genetic diversity enables experimental Ebola hemorrhagic fever pathogenesis |
|
