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Series GSE49562 Query DataSets for GSE49562
Status Public on Dec 31, 2014
Title Exploring the gene expression associated with Pten deficiency in the developing inner ear
Organism Mus musculus
Experiment type Expression profiling by array
Summary In our recent study, we reported the function of phosphatase and tensin homolog (PTEN) during inner ear development. PTEN is necessary for neuronal maintenance, such as neuronal survival and accurate nerve innervations of hair cells. To better understand the genes and signaling networks related to auditory neuron maintenance, we examined the profiles of differentially expressed genes (DEGs) using microarray analysis in Pten-deficient mice at E14.5. We identified 46 statistically significant DEGs using Significant Analysis of Microarrays (SAM) analysis with a false discovery rate (FDR) equal to zero. Among the DEGs, expression levels of candidate genes and expression domains were validated by quantitative real-time polymerase chain reaction (RT-PCR) and in situ hybridization, respectively. Ingenuity pathway analysis (IPA) with DEGs identified significant signaling networks associated with cellular movement and axon guidance. Significant networks revealed that Spp1-mediated cellular movement and G-protein signaling 4 (RGS4)-Akt are related with axon guidance. This result was consistent with the phenotypic defects of spiral ganglion in Pten conditional knockout (cKO) mice (e.g., abnormal migration of spiral ganglion and irregular formation of neuritis). From this study, we suggest two key regulatory signaling networks mediated by Spp1 and RGS4, which may play potential roles in neuronal differentiation of developing auditory neurons.
 
Overall design Embryonic day 14.5 inner ear tissues from Pten conditional knockout (cKO: Pax2Cre/+;PtenloxP/loxP) and littermate wild type (PtenloxP/+ and PtenloxP/loxP) were used (60 embryos of each group). Total RNA from three independent pools of inner ears from each group was extracted with TRIZOL, amplified using Ambion amplification kit, and cRNA (750 ng) was hybridized to Illumina MouseRef-8 v 2.0 Expression Bead Chips. Three biological replicates (three chips for wild-type samples and three chips for Pten cKO samples) were performed for microarray hybridization experiments.
 
Contributor(s) Kim H, Ryu J, Woo H, Cho SS, Sung M, Kim S, Park M, Park T, Koo S
Citation(s) 24893171
Submission date Aug 05, 2013
Last update date Oct 22, 2019
Contact name Hyung Jin Kim
E-mail(s) hjkim318@gmail.com
Phone +82-43-719-8617
Organization name Korea National Institute of Health
Department Division of Intractable Diseases, Center for Biomedical Sciences
Lab Intractable Diseases
Street address 187 Osongsaengmyeong 2-ro
City Osong-eup, Cheongwon-gun, Chungcheongbuk-do
ZIP/Postal code 363-951
Country South Korea
 
Platforms (1)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
Samples (6)
GSM1201833 Wild-type rep1
GSM1201834 Wild-type rep2
GSM1201835 Wild-type rep3
Relations
BioProject PRJNA214248

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
GSE49562_RAW.tar 3.1 Mb (http)(custom) TAR
GSE49562_non-normalized.txt.gz 1.0 Mb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table

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