Rattus norvegicus breed:Sprague-Dawley
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA320100 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3467239_subreads.fastq.gz | Fastqsanger.gz |
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Project description:Rattus norvegicus pineal gland between day and night Raw sequence reads
| PRJNA600669 | ENA
Project description:The cone-rod homeobox gene (Crx) encodes Crx, a transcription factor selectively expressed in two cell types, retinal photoreceptors and the melatonin secreting pinealocytes of the pineal gland. In this report the role of Crx in regulating gene expression in the mammalian pineal gland was extended using Affymetrix GeneChip technology. Deletion of Crx results in broad modulation of the mouse pineal transcriptome, including a >2-fold downregulation of 543 genes and a >2-fold upregulation of 745 genes. In addition to Crx, there was a >10-fold downregulation of 13 other genes. Of special interest was the discovery of a link between Crx and the homeobox gene Hoxc4, which was upregulated ~20-fold in the Crx-/- pineal gland. Analysis of night and day expression of genes indicated that a set of 51 genes exhibited differential expression in control animals. Of these genes, only eight were also differentially expressed in Crx-/- animals. This group included Aanat, which encodes the enzyme that controls the daily rhythm in melatonin synthesis in the vertebrate pineal gland. Accordingly, Crx appears to be essential for the 24-hour rhythmic component of expression of some genes in the pineal gland. In the Crx-/- mouse pineal gland, 41 genes exhibited differential night/day expression that was not seen in control animals, suggesting that Crx may function to modulate rhythmic expression of these genes as well. Together, the results of this investigation indicate that Crx broadly modulates the pineal transcriptome, perhaps in part through suppressive effects on expression of the homeobox gene Hoxc4.
2012-01-01 | GSE24625 | GEO
Project description:Biological processes are optimized by circadian and circannual biological timing systems. In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. At night, sympathetic input to the pineal gland, originating from the circadian clock in the suprachiasmatic nucleus, releases norepinephrine. This adrenergic stimulation causes an elevation of cAMP, which is thought to regulate many of the dramatic changes in genes expression known to occur at night. In many aspects, the adrenergic/cAMP effects on gene expression can be recapitulated in primary organ culture. We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. The pineal transcriptome was compared to that of other rat tissues processed in parallel. In addition, pineal glands were cultured in control conditions, or stimulated with norepinephrine, dibutyryl-cAMP (DBcAMP), or forskolin; the transcriptomes of these glands were then analyzed. Keywords: Time course (2 points) for in vivo pineal glands and various tissues; Treatment groups for cultured pineal glands
2009-01-15 | GSE12343 | GEO
Project description:Circular RNAs (circRNAs) are a new class of RNAs with covalently closed circular structures that are involved in many biological processes. However, information about circRNAs in the pineal gland is limited, especially in rats. In this study, 331 circRNAs were identified by the Illumina platform as being expressed in the pineal glands of rats during the night and day. Forty circRNAs with differential expression were found. A total of 737 GO terms were significantly enriched, and 121 KEGG pathways were found to contain differentially expressed genes. We predicted 6837 interactions between 65 cicRNAs and 549 miRNAs by using miRanda. We also found that high expression of miR-328a-3p in the daytime inhibits AANAT translation through targeting of the AANAT 3’UTR region. CircRNA-WNK2, which is highly expressed in the rat pineal gland during the night and functions as a miRNA sponge, removes this inhibitory effect and promotes the AANAT expression and melatonin secretion. The circadian expression profile of circRNAs in the rat pineal gland may provide more information on the roles of circRNAs in the regulation of melatonin circadian rhythm changes.
2020-03-03 | GSE146193 | GEO
Project description:Biological processes are optimized by circadian and circannual biological timing systems. In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. We have also used these data to characterize the non-rhythmic features of the transcriptome that set the pineal gland apart from other tissues by comparing them to the median expression in other rat tissues as found in the Genomics Institute of the Novartis Research Foundation (GNF), Entrez Gene Expression Omnibus (GEO) dataset GDS589. Experiment Overall Design: Rat pineal glands were obtained at mid-day and mid-night for RNA extraction and hybridization to Affymetrix microarrays. Triplicates of pooled pineal glands were analyzed at each timepoint.
2009-01-25 | E-GEOD-12341 | biostudies-arrayexpress
Project description:Biological processes are optimized by circadian and circannual biological timing systems. In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. Keywords: Time course (2 points)
2009-01-15 | GSE12342 | GEO
Project description:The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, as revealed earlier using Affymetrix GeneChip analysis. The retina is evolutionally related to the pineal gland so these two tissues share many gene expression patterns. This study more completely characterizes the temporally dynamic transcriptomes of these tissues using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, and coding transcripts not represented on the Affymetrix chips. We also identified transcripts that were selectively expressed in the pineal gland relative to other tissues by comparing pineal samples to a sample of pooled non-pineal tissues. The transcriptomes of the rat pineal gland and retina were sequenced using samples collected at 6 time points throughout a 24-hour cycle to identify rhythmically expressed transcripts. The transcriptomes of pools of mixed tissues collected at mid-day (ZT7) and mid-night (ZT19) were also sequenced for comparison to aid in determining pineal-enriched transcripts. Contributor: NISC, Comparative Sequencing Program
2014-02-05 | E-GEOD-46069 | biostudies-arrayexpress
Project description:Biological processes are optimized by circadian and circannual biological timing systems. In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. At night, sympathetic input to the pineal gland, originating from the circadian clock in the suprachiasmatic nucleus, releases norepinephrine. This adrenergic stimulation causes an elevation of cAMP, which is thought to regulate many of the dramatic changes in genes expression known to occur at night. In many aspects, the adrenergic/cAMP effects on gene expression can be recapitulated in primary organ culture. We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. The pineal transcriptome was compared to that of other rat tissues processed in parallel. In addition, pineal glands were cultured in control conditions, or stimulated with norepinephrine, dibutyryl-cAMP (DBcAMP), or forskolin; the transcriptomes of these glands were then analyzed. Experiment Overall Design: Total RNA was extracted from various rat tissues, and from both in vivo and cultured rat pineal glands, for processing and hybridization to Affymetrix microarrays. Quadruplicates of pooled in vivo pineal glands were analyzed at each timepoint. Single day and night samples of retina, cortex, cerebellum, hypothalamus, liver, and heart were analyzed. Triplicates of control and treated cultured pineal glands were analyzed.
2009-01-27 | E-GEOD-12343 | biostudies-arrayexpress
Project description:Biological processes are optimized by circadian and circannual biological timing systems. In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. We have also used these data to characterize the non-rhythmic features of the transcriptome that set the pineal gland apart from other tissues by comparing them to the median expression in other rat tissues as found in the Genomics Institute of the Novartis Research Foundation (GNF), Entrez Gene Expression Omnibus (GEO) dataset GDS589. Keywords: Time course (2 points)
2009-01-15 | GSE12341 | GEO
Project description:The zebrafish pineal gland (epiphysis) is an autonomous clock organ. In addition to being a site of melatonin production, it contains photoreceptor cells and functions as a circadian clock pace maker, making zebrafish a useful model system to study the developmental control of expression of genes associated with melatonin synthesis and photodetection, and the circadian clock. Here we have used DNA microarray technology to study the zebrafish pineal transcriptome. Analysis of gene expression at five different developmental stages (three embryonic and two adult) has revealed a highly dynamic transcriptional profile, revealing many genes that are highly expressed in the pineal gland. Statistical analysis of the data based on Gene Ontology (GO) annotation indicates that many transcription factors and cell cycle genes are highly expressed during embryonic stages, whereas genes dedicated to visual system signal transduction are preferentially expressed in the adult. Furthermore, several genes were identified that exhibit day/night differences in expression. Our data provide a rich source of candidate genes for distinct functions at different stages of pineal gland development. Experiment Overall Design: Adults and embryos were kept under a 14-hr-light/10-hr-dark cycle. Pineal glands were isolated manually, guided by GFP fluorescence, from embryonic (3d, 5d, and 10d) and adult (3 month and 1-2 yr) transgenic zebrafish in which expression of the GFP gene is driven by the pineal-specific aanat2 promoter. For comparison, brain tissue from which the pineal gland and eyes had been removed was also collected (referred to as “brain”). Altogether, we collected 20 types of samples: five time points (3d, 5d, 10d, 3 mo, and 1-2 yr), two organs (pineal gland and brain), and two sampling times (day and night). For each type of sample, tissue was obtained and processed three to five times. Total RNA was prepared from each sample using the RNeasy Lipid Tissue Mini Kit (Qiagen) and biotin-labeled cDNA was generated using the Ovation Biotin system kit (NeuGen). The Affymetrix GeneChip® Zebrafish Genome Array was hybridized and processed using the standard Affymetrix protocol.
2009-10-30 | E-GEOD-13371 | biostudies-arrayexpress