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Sample GSM1687490 Query DataSets for GSM1687490
Status Public on May 16, 2015
Title IM102_691_2d_RNA_4
Sample type RNA
 
Source name Lung tissue, 691-inoculated, 2 day(s), bioreplicate 4
Organism Mus musculus
Characteristics strain: C57Bl/6J
tissue: lung
age: 22 weeks
time (d.p.i.): 2
virus: 691
biological_replicate: 3
Treatment protocol Mice were anesthetized with isofllurane and inoculated with PBS or PBS containing virus in a volume of 50 μl.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from Trizol.
Label Cy3
Label protocol Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.
 
Hybridization protocol Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
Scan protocol The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
Data processing Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the two biological replicates was performed independently of the other.
 
Submission date May 15, 2015
Last update date Aug 31, 2016
Contact name Natalie Heller
E-mail(s) natalie.heller@pnnl.gov
Organization name PNNL
Street address 902 Battelle Blvd.
City Richland
ZIP/Postal code 99354
Country USA
 
Platform ID GPL11202
Series (2)
GSE65575 Modeling Host Responses to Understand Severe Human Virus Infections
GSE68945 Mouse lung tissue transcriptome response to a wild type infectious clone of H7N9 Influenza virus and mutant H7N9 viruses [mRNA]

Data table header descriptions
ID_REF
VALUE Quantile normalized signal

Data table
ID_REF VALUE
A_55_P1989846 10.95878292
A_55_P1991598 7.258985808
A_55_P2022211 14.24700061
A_55_P1980764 7.558437568
A_55_P1964375 10.82367692
A_51_P128876 16.73326281
A_55_P2121042 7.379018389
A_52_P219230 8.112253652
A_51_P207591 13.73479556
A_55_P2131920 9.105547064
A_55_P2404223 8.455667363
A_55_P2101944 14.3651302
A_52_P358860 10.50208417
A_51_P119031 10.81839969
A_51_P309854 7.891220179
A_51_P343900 11.18908984
A_51_P234359 8.493775045
A_51_P487813 13.71573903
A_52_P613977 12.70398637
A_55_P1957209 9.705593453

Total number of rows: 39429

Table truncated, full table size 981 Kbytes.




Supplementary file Size Download File type/resource
GSM1687490_IM102_691_2d_RNA_4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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