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RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio
- Source :
- BMC Genomics, Vol 21, Iss 1, Pp 1-13 (2020), BMC Genomics
- Publication Year :
- 2019
- Publisher :
- Research Square Platform LLC, 2019.
-
Abstract
- Background Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6c (pde6c) mutant. Results The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the log fold change (logFC) (±4) and p-values (p Conclusions Our data strongly indicate that, among these genes, the above-mentioned pathways’ genes as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.
- Subjects :
- Retinal degeneration
FastQC
Light Signal Transduction
genetic structures
Trinity
lcsh:QH426-470
lcsh:Biotechnology
Neural degeneration
Retina
03 medical and health sciences
Pde6c
0302 clinical medicine
lcsh:TP248.13-248.65
Gene expression
Genetics
medicine
Animals
Gene Regulatory Networks
RNA-Seq
KEGG
Zebrafish
Gene
030304 developmental biology
0303 health sciences
Cyclic Nucleotide Phosphodiesterases, Type 6
Retinal pigment epithelium
biology
Retinal Degeneration
Zebrafish Proteins
biology.organism_classification
medicine.disease
Cell biology
lcsh:Genetics
medicine.anatomical_structure
Mutation
Gene ontology
030217 neurology & neurosurgery
Biotechnology
Visual phototransduction
Research Article
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- BMC Genomics, Vol 21, Iss 1, Pp 1-13 (2020), BMC Genomics
- Accession number :
- edsair.doi.dedup.....a9ae8bcb87aede70d3392df25f9e7f41