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Sample GSM2419082 Query DataSets for GSM2419082
Status Public on Jan 03, 2017
Title Sp_W_D4_16680x8016_m69
Sample type RNA
 
Source name Spleen Tissue from West Nile Virus infected Line 16680x8016 at Day 4 post infection
Organism Mus musculus
Characteristics batch: 2
Sex: m
tissue: Spleen
collaborative cross line (genetic background): 16680x8016
animal number (rxid): m69
treatment: West Nile Virus infected
days post-infection: 4
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 4 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

Data table header descriptions
ID_REF
VALUE log2 transformed RMA

Data table
ID_REF VALUE
17210850 1.111850776
17210852 1.912314727
17210855 8.218687866
17210869 6.017478625
17210883 1.581742614
17210887 7.270886994
17210904 2.918462972
17210912 8.235357676
17210947 2.116103277
17210953 3.760421549
17210984 7.60202192
17210994 3.190086116
17210996 3.753356197
17210998 1.612776014
17211000 4.988143922
17211004 4.516017667
17211023 2.459042951
17211033 3.819858546
17211043 9.301961983
17211066 3.921000382

Total number of rows: 29361

Table truncated, full table size 598 Kbytes.




Supplementary file Size Download File type/resource
GSM2419082_16680x8016_m69_Sp.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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