Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA390613 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5687190_1.fastq.gz | Fastqsanger.gz | |||
| SRR5687190_2.fastq.gz | Fastqsanger.gz | |||
| SRR5687191_1.fastq.gz | Fastqsanger.gz | |||
| SRR5687191_2.fastq.gz | Fastqsanger.gz | |||
| SRR5687192_1.fastq.gz | Fastqsanger.gz |
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Project description:The rd1 mouse retina is a well-studied model of retinal degeneration where rod photoreceptors undergo cell death beginning at postnatal day P10 until P21. This period coincides with photoreceptor terminal differentiation in a normal retina. We have used the rd1 retina as a model to investigate early molecular defects in developing rod photoreceptors prior to the onset of degeneration. Using a microarray approach, we performed gene profiling comparing rd1 and wild type retinas at four time points starting at P2, prior to any obvious biochemical or morphological differences, and concluding at P8, prior to the initiation of cell death. We have identified genes that are differentially regulated in the rd1 retina at early time points, which may give insights into developmental defects that precede photoreceptor cell death. This is the first report of PRA1 expression in the retina. Our data support the hypothesis that PRA1 plays an important role in vesicular trafficking between the Golgi and cilia in differentiating and mature rod photoreceptors. Retinal samples were harvested from both rd1/le and wt animals at postnatal days 2, 4, 6, and 8 for microarray. Each sample included 8-14 retinas and experiments were performed in quadruplicate. Ten micrograms of total RNA was used for cDNA systhesis in target molecule production.
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Project description:Control of neural organogenesis is a complex process and the epigenetic contribution is largely unknown. Here we have followed the genome-wide distribution of two important histone H3 modifications, H3K4me2 and H3K27me3 during late mouse retina development. We found that genes expressed only in mature rod photoreceptors, have a unique signature consisting of de-novo accumulation of H3K4me2 both at the transcription start site (TSS) and over the whole gene that correlates with the increase in transcription, but no accumulation of H3K27me3 at any stage. We also found that distribution of H3K4me2 and H3K27me3 on the genes widely expressed is not always associated with their transcriptional levels. Genes without H3K4me2 and H3K27me3 accumulation at any stage represent a group of transcripts never expressed in retina. The epigenetic signatures defined by H3K4me2 and H3K27me3 can distinguish cell-type specific genes from widespread transcripts and may be reflective of cell specificity during retina maturation. Examination of 2 different histone modifications during late mouse retina development.
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Project description:Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish, an important animal model for vision science. Methods: Zebrafish rods, and non-rod retinal cells of the XOPS:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas, and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01, 597 transcripts were upregulated in rods vs. non-rod retinal cells, and 1032 were downregulated. 13,324 total transcripts were detected in rods, including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics.
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