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Sample GSM1687532 Query DataSets for GSM1687532
Status Public on May 16, 2015
Title IM102_Lung_F/M_2d_miRNA_2
Sample type RNA
 
Source name Lung tissue, FM-inoculated, 2 day(s), bioreplicate 2
Organism Mus musculus
Characteristics strain: C57Bl/6J
tissue: lung
age: 22 weeks
time: 2d
virus: FM
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).
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 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 GPL19970
Series (2)
GSE65575 Modeling Host Responses to Understand Severe Human Virus Infections
GSE68946 Mouse lung tissue transcriptome response to a wild type infectious clone of H7N9 Influenza virus and mutant H7N9 viruses [microRNA]

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
A_54_P00004775 6.874108417
A_54_P1612 6.021888828
A_54_P2025 5.873376285
A_54_P2260 12.42093541
A_54_P00004550 6.943028066
A_54_P1839 5.949536385
A_54_P4391 9.171038577
A_54_P00004682 5.970219597
A_54_P3543 6.710692904
A_54_P00006037 6.032534313
A_54_P2360 7.121856496
A_54_P2569 6.116896163
A_54_P00004884 6.014794268
A_54_P2483 11.56568202
A_54_P00005990 6.30261343
A_54_P00005610 5.915101919
A_54_P00005262 5.913272108
A_54_P00005141 6.026081062
A_54_P00005870 5.953270751
A_54_P00005045 5.878242526

Total number of rows: 3105

Table truncated, full table size 75 Kbytes.




Supplementary file Size Download File type/resource
GSM1687532_IM102_FM_2d_RNA_2.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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