Transcription profiling of rat pineal gland, Expt B
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
SUBMITTER: David Klein
PROVIDER: E-GEOD-12342 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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. 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. Keywords: Time course (2 points)
2009-01-15 | GSE12342 | 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: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 rat pineal gland is a highly dynamic tissue with many hundreds of genes changing more than two-fold in a 24-hr daily rhythm as measured by Affymetrix GeneChip analysis. We sought to more completely understand this dynamic transcriptome using RNA-Seq in order to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, etc. We also wished to identify transcripts that were selectively expressed in the pineal glands relative to other tissues. Toward this end we performed RNA-Seq on three types of samples; 1) a pool of pineal glands sampled at mid-day (ZT7); 2) a pool of pineal glands sampled at mid-night (ZT19); and a pool of 15 different tissues collected from 3 animals at mid-day (ZT7). Animals were housed in a 14:10 light:dark lighting cycle. PolyA-selected RNA was fragmented and sequenced on an Illumina GAII machine, yielding paired-end 51-mer reads.
2015-03-23 | GSE45654 | 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:The transcriptome of the rat pineal gland is highly dynamic, with many hundreds of genes changing more than two-fold on a 24-hr daily rhythm, as revealed earlier using Affymetrix GeneChip analysis. Several key transcription factors and enzymes are known to change dramatically during development of the pineal gland. Studies on a small number of genes indicate that the onset of rhythmic expression generally occurs later in development. This study characterizes this temporally dynamic transcriptome 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. The rat pineal transcriptome was sequenced in samples from four ages, from embryonic day 21 through adult. At each age, samples were taken at mid-day and mid-night. Data were collected to describe the changes in the developing pineal transcriptome and to identify transcripts that exhibit day/night differences in expression at each age.
2014-10-24 | E-GEOD-46127 | biostudies-arrayexpress
Project description:The vertebrate pineal gland is dedicated to the production of the hormone melatonin, which increases at night to influence circadian and seasonal rhythms. This increase is associated with dramatic changes in the pineal transcriptome. Here, single-cell analysis of the rat pineal transcriptome was approached by sequencing mRNA from ~17,000 individual pineal cells, with the goals of profiling the cells that comprise the pineal gland and examining the proposal that there are two distinct populations of pinealocytes differentiated by the expression of Asmt, which encodes the enzyme that converts N-acetylserotonin to melatonin. In addition, this analysis provides evidence of cell-specific time-of-day dependent changes in gene expression. Nine transcriptomically distinct cell types were identified: ~90% were classified as melatonin-producing α- and β-pinealocytes (1:19 ratio). Non-pinealocytes included three astrocyte subtypes, two microglia subtypes, vascular and leptomeningeal cells, and endothelial cells. α-Pinealocytes were distinguished from β-pinealocytes by ~3-fold higher levels of Asmt transcripts. In addition, α-pinealocytes have transcriptomic differences that likely enhance melatonin formation by increasing the availability of the Asmt cofactor S-adenosylmethionine, resulting from increased production of a precursor of S-adenosylmethionine, ATP. These transcriptomic differences include ~2-fold higher levels of the ATP-generating oxidative phosphorylation transcriptome and ~8-fold lower levels of the ribosome transcriptome, which is expected to reduce the consumption of ATP by protein synthesis. These findings suggest that α-pinealocytes have a specialized role in the pineal gland: efficiently O-methylating the N-acetylserotonin produced and released by β-pinealocytes, thereby improving the overall efficiency of melatonin synthesis. We have also identified transcriptomic changes that occur between night and day in seven cell types, the majority of which occur in β-pinealocytes and to a lesser degree in α-pinealocytes; many of these changes were mimicked by adrenergic stimulation with isoproterenol. The cellular heterogeneity of the pineal gland as revealed by this study provides a new framework for understanding pineal cell biology at single-cell resolution.
2018-10-05 | GSE115723 | 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