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Analysis of gene expression profiling of normal retina and brain cortices

ABSTRACT: Using a canine custom retinal cDNA microarray our aim is to identify normal gene expression profiling for retina and frontal, occipital and temporal brain cortices Keywords: retina-brain comparisons

ORGANISM(S): Canis lupus familiaris

PROVIDER: GSE5208 | GEO | 2006/07/06

SECONDARY ACCESSION(S): PRJNA96497

REPOSITORIES: GEO

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Project description:The objective of the study was to examine the gene expression changes in the medial frontal cortices of P28 offspring from the breeding of Dnmt3l conditional knockin and Emx1-cre mice, strain of C57BL/6J. There were 12 samples in total- A-1, A-2, A-3, B-1, B-2, B-3, C-1, C-2, C-3, D-1, D-2, and D-3. A-1 to A-3 and B-1 to B-3 were medial frontal cortices from the male and female Emx1-cre mice respectively, which were used as the control groups (CON). C-1 to C-3 and D-1 to D-3 were medial frontal cortices from the male and female Dnmt3l overexpression mice respectively, which were used as the experimental groups (OE). The total RNA of each sample was extracted from the medial frontal cortices by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. There were two types of libraries: the circRNA, mRNA, and lncRNA were all constructed by removing rRNA (one library, three types of RNA were analyzed together), and the insert fragment was about 300bp; the small RNA was constructed and analyzed separately, mainly microRNA of about 22bp. Results: among 119414 cleaned mRNAs, 3015 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). The differential expressed genes distributed in all chromosomes. Functional annotation with GO and KEGG enrichment revealed the top functional groups including ATP binding, zinc ion binding, glutamatergic synapse, dopaminergic synapse, MAPK signaling pathway, and PI3K-Akt signaling pathway. Among 23698 lncRNAs, 658 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). Among 10673 circRNAs, 49 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). Among 1821 microRNAs, 101 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold).

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Analysis of gene expression profiling of normal retina and brain cortices

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