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Sample GSM1713654 Query DataSets for GSM1713654
Status Public on Jun 18, 2015
Title IM101_CA04_2d_RNA_2
Sample type RNA
Source name Lung_CA04-inoculated_2 days
Organism Mus musculus
Characteristics strain: C57Bl/6J
age: 22 weeks
virus: CA04
time (d.p.i): 2
tissue: lung
biological_replicate: 2
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 homogenate of mouse lung.
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).
Description IM101_CA04_2d_2
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 biological replicates was performed independently of the other.
Submission date Jun 17, 2015
Last update date Aug 31, 2016
Contact name Natalie Heller
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
GSE69945 Mouse lung tissue transcriptome response to H1N1, H5N1, and mutants [mRNA]

Data table header descriptions
VALUE normalized

Data table
A_55_P1989846 9.863058555
A_55_P1991598 6.962917066
A_55_P2022211 14.47379102
A_55_P1980764 7.122498424
A_55_P1964375 10.05552443
A_51_P128876 16.51328345
A_55_P2121042 8.176023716
A_52_P219230 7.063208138
A_51_P207591 12.50632562
A_55_P2131920 9.37894588
A_55_P2404223 7.609990301
A_55_P2101944 14.42461884
A_52_P358860 8.160942968
A_51_P119031 10.15914259
A_51_P309854 7.627557304
A_51_P343900 10.74104427
A_51_P234359 7.880572798
A_51_P487813 13.87334239
A_52_P613977 11.6361552
A_55_P1957209 8.441450215

Total number of rows: 39429

Table truncated, full table size 981 Kbytes.

Supplementary file Size Download File type/resource
GSM1713654_IM101_CA04_2d_RNA_2.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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