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Next Generation Sequencing Study of Circadian Changes in Transcriptome of Human Pineal Gland

ABSTRACT: Purpose: We performed an NGS study on the circadian changes in human pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock, as well as to conduct a comparative analysis of pineal transcriptomes of several animal species. Methods: Total RNA from human pineal glands of individuals that died at 2 timepoints (Mid-Day, Midnight) was deep sequenced, using Illumina HiSeq2500. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in human pineal gland. Conclusions: Our study represents part of a comparative analysis of pineal gland transcriptome of several species, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE100472 | GEO | 2018/02/01

REPOSITORIES: GEO

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Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye

Project description:Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly-A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints (Mid-Day, Midnight) was deep sequenced, using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinal(eye) and pineal gland transcriptome of several species, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2018-02-01 | GSE99285 | GEO

Next Generation Sequencing Study of Circadian Changes in Transcriptome of Rhesus Macaque Pineal Gland and Retina

Project description:Purpose: We performed an NGS study on the circadian changes in Rhesus Macaque retina and pineal gland transcriptome in order to elucidate novel elements in the primate circadian clock. Methods: Total RNA from retina and pineaal glands of Rhesus Macauqes euthanized at 4 timepoints (Dawn, Day, Dusk and Night) was deep sequenced, in triplicate, using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of novel genes that show circadian activivty in both retina and pineal gland of the Rhesus Macaque. A particular set of genes involved in the production of N-acetyltryptamine in Rhesus Macaque retina appears to be responsible for the circadian oscillations of the concentrations of N-acetyltriptamine in the plasma, thereby accentuating N-acetyltriptamine as a retina derived signaling molecule in primates. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2017-06-01 | GSE78165 | GEO

Transcriptome analysis of pineal glands in a mouse model of Alzheimer’s disease

Project description:The pineal gland maintains the circadian rhythm in the body by secreting the hormone melatonin. Alzheimer’s disease (AD) is the most common neurodegenerative disease. Pineal gland impairment in AD is widely observed, but no study to date has analyzed the transcriptome in the pineal glands of AD. To establish resources for the study on pineal gland dysfunction in AD, we performed a transcriptome analysis of the pineal glands of AD model mice and compared them to those of normal mice. There were diverse protein-coding RNAs, long noncoding RNAs and circular RNAs with global change in the pineal glands of AD mouse model. The analyzed data reported in this study will be an important resource for future studies to elucidate the altered physiology of the pineal gland in AD.

2019-12-31 | GSE129586 | GEO

Temporal expression data from zebrafish pineal gland

Project description:Microarray data allowed detection of genes that have circadian expression pattern in the zebrafish pineal gland

2012-10-19 | GSE41696 | GEO

Transcriptome analysis of the zebrafish pineal gland

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. Keywords: time course

2009-10-27 | GSE13371 | GEO

Light and rhythmic regulation of gene expression in pineal gland of the chicken

Project description:Light is the primary environmental cue in resetting the phase of circadian pacemaker in vertebrates. In birds, the effect of light is partly mediated by modulating the levels of circadian genes in the pineal gland. To further elucidate the mechanism by which light resets the circadian clock, we studied gene expression in the chicken pineal gland under acutely extended light period.

2015-06-30 | GSE34017 | GEO

Transcription profiling of rat pineal Expt C

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

Transcription profiling of rat pineal Expt A

2009-01-25 | E-GEOD-12341 | biostudies-arrayexpress

Transcription profiling of zebrafish pineal gland

Project description:Microarray data allowed detection of genes that are highly expressed in the pineal gland. Experiment Overall Design: Adult Tg(aanat2:EGFP)Y8 transgenic zebrafish in which EGFP marks the pineal gland were used for RNA extraction and hybridization on Affymetrix microarrays. Fish were anesthetized in 1.5 mM Tricane (Sigma) and sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. Since the pineal gland is a clock-containing organ and levels of certain transcripts may vary throughout the circadian cycle, glands were collected throughout the 24-hr cycle at 4 hr intervals. During the 24-hr cycle the fish were either maintained in a 12-h light/12-h dark cycle (LD) or kept in constant darkness (DD). 12 pineal glands were collected and pooled at each time point at each light condition, and total RNA was extracted (RNeasy, Qiagen).

2009-05-11 | E-GEOD-13196 | biostudies-arrayexpress

Temporal expression data from zebrafish pineal gland

Project description:Microarray data allowed detection of genes that have circadian expression pattern in the zebrafish pineal gland Adult (0.5-1.5 years old) transgenic zebrafish, Tg(aanat2:EGFP)Y8, which express enhanced green fluorescent protein (EGFP) in the pineal gland under the control of the aanat2 regulatory regions, were used. Fish were raised under 12-hr light:12-hr dark (LD) cycles, in a temperature controlled room, and transferred to constant darkness (DD) for tissue collection. Fish were anesthetized in 1.5 mM Tricane (Sigma), sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time (CT) 14, pineal glands were collected at 4-hr intervals for 48 hours (12 time points identified as CT 14, 18, 22, 2, 6, 10, 14b, 18b, 22b, 2b, 6b and 10b). Pools of 12 pineal glands were prepared at each time-point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (QIAGEN), according to the manufacturer's instructions.

2012-10-19 | E-GEOD-41696 | biostudies-arrayexpress

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