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Sample GSM1246916 Query DataSets for GSM1246916
Status Public on Apr 02, 2014
Title IM015_RIPK3_Mock_d2_1
Sample type RNA
Source name IM015_RIPK3_Mock_d2
Organism Mus musculus
Characteristics tissue: Lung
mouse strain: RIPK3 knock-out
infection: Mock
Treatment protocol Lung tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation overnight, samples were stored at -80ºC until processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.
Extracted molecule total RNA
Extraction protocol All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.
Label Cy3
Label protocol The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
Hybridization protocol The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.
Scan protocol Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.
Data processing Raw images were analyzed using the Agilent Feature Extraction software (version and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.
Submission date Oct 22, 2013
Last update date Apr 02, 2014
Contact name Michael Katze
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 GPL7202
Series (1)
GSE51526 IM015 - Influenza infection of C57BL6 and RIPK3 knock-out mice

Data table header descriptions
VALUE Normalized log2 expression values for probes passing Agilent QC flags

Data table
A_51_P100021 7.489450555
A_51_P100034 12.76498411
A_51_P100063 9.068708701
A_51_P100084 7.063409458
A_51_P100099 10.60520925
A_51_P100155 11.6881687
A_51_P100174 10.94831706
A_51_P100181 9.322275715
A_51_P100227 10.6910676
A_51_P100246 11.19436804
A_51_P100289 11.96770145
A_51_P100298 9.69900784
A_51_P100327 9.063563227
A_51_P100347 5.97171987
A_51_P100379 6.945955236
A_51_P100428 6.508566115
A_51_P100470 6.088007713
A_51_P100505 10.37374014
A_51_P100537 6.74731845
A_51_P100565 12.10855797

Total number of rows: 31957

Table truncated, full table size 775 Kbytes.

Supplementary file Size Download File type/resource
GSM1246916_US93503719_251486838858_S01_GE1_107_Sep09_1_2.txt.gz 8.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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