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Sample GSM1909270 Query DataSets for GSM1909270
Status Public on Dec 31, 2015
Title CASTd3_4 lung
Sample type RNA
 
Source name lung
Organism Mus musculus
Characteristics infection: d3 pi
strain: CAST/EiJ
Treatment protocol The CC founder (C57BL/6J, 129S1/SvlmJ, CAST/EiJ, PWK/PhJ) were intranasally infected with influenza A/HK/01/68 (H3N2) with 20μl virus solution (1x101 ffu) or mock infected (with PBS).
Extracted molecule total RNA
Extraction protocol RNA was prepared using Qiagen RNAeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Oct 15, 2015
Last update date Dec 31, 2015
Contact name Robert Geffers
E-mail(s) robert.geffers@helmholtz-hzi.de
Phone +49 531-6181-3058
Organization name HCI - Helmholtz Centre for Infection Research
Department Dep. Molecular Bacteriology
Lab Genome Analytics
Street address Inhoffenstr. 7
City Braunschweig
ZIP/Postal code 38124
Country Germany
 
Platform ID GPL11202
Series (2)
GSE74074 Influenza H3N2 infection of the Collaborative Cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice (lung)
GSE74077 Influenza H3N2 infection of the Collaborative Cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice

Data table header descriptions
ID_REF
VALUE Bckground subtracted, log2 transformed, normalized (quantile)

Data table
ID_REF VALUE
A_55_P1989846 10.135
A_55_P2022211 13.594
A_55_P1964375 11.403
A_51_P128876 17.079
A_55_P2121042 6.278
A_52_P219230 6.253
A_51_P207591 14.354
A_55_P2131920 8.476
A_55_P2404223 8.428
A_55_P2101944 15.138
A_52_P358860 10.001
A_51_P119031 9.276
A_51_P309854 6.196
A_51_P343900 12.006
A_51_P234359 11.914
A_51_P487813 12.328
A_52_P613977 11.85
A_55_P1957209 7.869
A_52_P549166 8.288
A_55_P2052210 14.193

Total number of rows: 32044

Table truncated, full table size 618 Kbytes.




Supplementary file Size Download File type/resource
GSM1909270_252665516868_Kollmus1024_S01_GE1_107_Sep09_1_4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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