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Series GSE50644 Query DataSets for GSE50644
Status Public on Sep 06, 2013
Title Analysis of miRNA expression in lung (CC10) VEGF transgenic mice and their wild type litters
Organism Mus musculus
Experiment type Non-coding RNA profiling by array
Summary Vascular Endothelial Growth Factor (VEGF) is a critical regulator of pulmonary Th2 inflammation but the underlying mechanism and the roles of miRNAs in this process have not been defined. We analyzed the effect of VEGF on lung microRNAs by microarray analysis and validated the findings by Taqman qRT-PCR. We compared the levels of microRNAs in the lungs of transgenic mice with their wild type litters after overexpression of VEGF from a lung epithelium-restricted transgene. VEGF was overexpressed in the lung epithelium of CC10-rtTA-VEGF transgenic mice by adding Doxycycline to their drinking water for 7-10 days. RNA from the lungs of VEGF transgenic mice and their wild type litters were extracted and analyzed by microarray. The expression levels of microRNAs that were significanly altered were validated in another group of mice.
 
Overall design Lung RNA from each transgenic mouse was labeled with Cy5 and lung RNA from wild type mice were labeled with Cy3. The two labeled RNAs were hybridized to the miRNA array. This array (chip ID 01_M9.1_070362) detects miRNA transcripts listed in Sanger miRBase Release 9.1 (http://www.sanger.ac.uk/Software/Rfam/mirna/). Multiple control probes are included in each chip. The control probes are used for quality controls of chip production, sample labeling and assay conditions. Among the control probes, PUC2PM-20B and PUC2MM-20B are the perfect match and single-based match detection probes, respectively, of a 20-mer RNA positive control sequence that is spiked into the RNA samples before labeling. One may assess assay stringency from the intensity ratio of PUC2PM-20B and PUC2MM-20B, which is normally larger than 30. When the option for custom probes is selected, custom probes are also included. After hybridization three imaged were obtained. From Cy3 and Cy5 images one may directly read miRNA profiles and from Ratio images one may get a quick sense of differential expressions between the corresponding samples. The images are displayed in pseudo colors so as to expand visual dynamic range. In the Cy3 and Cy5 intensity images, as signal intensity increases from 1 to 65,535 the corresponding color changes from blue to green, to yellow, and to red. In the Cy3/Cy5 ratio image, when Cy3 level is higher than Cy5 level the color is green; when Cy3 level is equal to Cy5 level the color is yellow; and when Cy5 level is higher than Cy3 level the color is red.
 
Contributor(s) Takyar S
Citation(s) 24043765
Submission date Sep 06, 2013
Last update date Oct 22, 2013
Contact name seyedtaghi takyar
E-mail(s) seyedtaghi.takyar@yale.edu
Organization name Yale School of Medicine
Department Medicine
Street address 300 Cedar street
City New haven
State/province CT
ZIP/Postal code 06519
Country USA
 
Platforms (1)
GPL17685 LC Sciences Mouse 01_M9.1_070362 miRNA Array
Samples (1)
GSM1225244 Lung_6-8 weeks_CC10 VEGF 10 days_rep1
Relations
BioProject PRJNA218408

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE50644_ProcessedData_signal_log2ratio.txt.gz 76.7 Kb (ftp)(http) TXT
GSE50644_RAW.tar 100.0 Kb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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