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Sample GSM2419044 Query DataSets for GSM2419044
Status Public on Jan 03, 2017
Title Sp_W_D4_8010x16441_99
Sample type RNA
 
Source name Spleen Tissue from West Nile Virus infected Line 8010x16441 at Day 4 post infection
Organism Mus musculus
Characteristics batch: 1
Sex: m
tissue: Spleen
collaborative cross line (genetic background): 8010x16441
animal number (rxid): 99
treatment: West Nile Virus infected
days post-infection: 4
collaborative cross line (genetic background, unc_id): CC(013x041)/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 1.176284503
17210852 2.191430689
17210855 8.639417966
17210869 5.858418233
17210883 2.478537507
17210887 6.89719204
17210904 2.849122101
17210912 8.204903788
17210947 1.872881216
17210953 3.386692229
17210984 7.747041623
17210994 2.978256189
17210996 3.972988458
17210998 1.697638373
17211000 2.584179882
17211004 4.911175328
17211023 1.198387449
17211033 4.0168496
17211043 9.152766716
17211066 3.984157426

Total number of rows: 29361

Table truncated, full table size 599 Kbytes.




Supplementary file Size Download File type/resource
GSM2419044_8010x16441_99_m_Sp_G_W_D4.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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