Integration of zebrafish pineal transcriptomes reveals cell type-specific timing
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE333181 | GEO | 2026/06/01
REPOSITORIES: GEO
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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
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
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
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. Three paradigms of treatments were used in this study. For each paradigm, chicks were assigned at random to control treatment (control groups) or light treatment (light groups). All birds in control groups were given 12 h light and 12 h dark period (LD 12:12). Light-on time is referred to as Zeitgeber Time 0 (ZT0). In paradigm 1, birds in the light group (n =25 for each of the groups in each paradigm) were acclimated to LD 12:12 for one week in the same light scheme as were the control birds, then exposed to light for 2 h during the subjective late night (ZT22 to ZT24) on the last day. All birds (including the controls) were sacrificed at ZT0. Pineal glands were dissected and 5-6 pineal glands were pooled for the preparation of one RNA sample. In paradigm 2, birds in the light group were acclimated as in paradigm 1 for one week, then exposed to light for 2 h during the early subjective night (ZT12 to ZT14) on the last day. All birds (including controls) were sacrificed at ZT14. The pineal glands were also pooled as before. In paradigm 3, birds in the light group (n = 25) were kept in LD 15:9 cycle all the time, and all birds (including controls) were sacrificed at ZT14. Similarly, 5-6 pineal glands in the same treatment were pooled.
2015-06-30 | E-GEOD-34017 | biostudies-arrayexpress
Project description:Disruption of the physiologic sleep-wake cycle and low melatonin levels frequently accompany cardiac disease, yet the underlying mechanism has remained enigmatic. Immunostaining of sympathetic axons in optically cleared pineal glands from humans and mice with cardiac disease revealed their substantial denervation compared to controls. Spatial, single-cell, nuclear, and bulk RNA sequencing traced this defect back to the superior cervical ganglia (SCG), which responded to cardiac disease with accumulation of inflammatory macrophages, fibrosis, and the selective loss of pineal gland-innervating neurons. Depletion of macrophages in the SCG prevented disease-associated denervation of the pineal gland and restored physiological melatonin secretion. Our data identify the mechanism underlying the disturbance of diurnal rhythmicity in cardiac disease and suggest means for therapeutic intervention.
2023-07-20 | GSE231764 | GEO
Project description:Microarray data allowed detection of genes that have circadian expression pattern in the zebrafish pineal gland
2012-10-19 | GSE41696 | GEO
Project description:There is growing appreciation that the feeling of well-being, alterations in mood and susceptibility to a variety of medical disorders depend on the proper expression of the master circadian clock and the synchrony among the other oscillators found in many peripheral tissues. To improve our understanding of the role of peripheral oscillators, an improved understanding of the molecular machinery sub-serving the circadian variation in gene expression is essential. Our long-term goal is to understand the molecular mechanisms that initiate circadian gene expression following external stimulation in the mammalian pineal gland. Are all or just some of the "circadian clock" genes induced by NE, cAMP, or cGMP? In this project we compare a series of gene expression patterns using DNA microarray in response to cAMP, cGMP and NE stimulation to understand why NE does not initiate circadian rhythms in the rat pineal gland. As a preliminary experiment we will compare gene expression 0, 1, and 4 h after start of chemical stimulation. A failure of NE to initiate circadian rhythms is due to failure of activation of certain "circadian clock" genes. We found that circadian rhythms are initiated by stimulation of cAMP or cGMP analogue in the rat pineal gland, while norepinephrine (NE) stimulation only moderately induce Period1 mRNA (one of "circadian clock" genes) 24 h after start of stimulation. From these results we hypothesize that external stimulation activates some "circadian clock" genes simultaneously, and that failure of circadian rhythm initiation following NE stimulation is due to insufficient "circadian clock" genes activations. Male rats of wistar strain are kept in 12h-12h light dark cycles at least for one week before start of experiments. Pineal glands are removed from animals and placed in the culture dish. Rat pineal glands are cultured for 3 days before chemical stimulation. On the day of experiment, the pineal cultures are stimulated using one of NE, cAMP and cGMP analogues for 1 or 4 h before harvest. The samples are immediately frozen and total RNA are extracted from each group which are from a pool of 8 pineal glands using Trizol reagent (Invitrogen). Concentrations of total RNA are determined using spectrophotometer, and six microgram of total RNA is aliquoted in each sample tube for further analysis. Since we already have Affymetrix Rat Genome U34A array GeneChips, we would like to send Chips as well as our total RNA samples. Experiment Overall Design: as above
2008-06-12 | E-GEOD-2865 | biostudies-arrayexpress
Project description:The pineal gland regulates circadian rhythms through melatonin production, yet human studies are limited by poor tissue access. To overcome this, we developed human pineal gland organoids (hPGOs) from pluripotent stem cells, modeling pineal development and function. Single-cell RNA sequencing revealed distinct mature and developing pinealocyte populations with transcriptomic profiles closely resembling the in vivo pineal gland. hPGOs produce melatonin, express adrenergic receptors, and respond to noradrenaline, mimicking physiological regulation. To model disease-related impairments, we generated hPGOs from Angelman syndrome (AS) patient-derived iPSCs, which exhibit disrupted pinealocyte differentiation and markedly reduced melatonin synthesis, reflecting AS-related developmental pathology. Additionally, transplanted hPGOs restored circulating melatonin in pinealectomized mice, demonstrating their potential for cell-therapy approaches. These findings establish hPGOs as a robust platform for probing pineal development, circadian regulation, and their disruption in neurodevelopmental and sleep-related disorders.
2026-01-20 | GSE290048 | GEO
Project description:Light has a strong effect on whole organism physiology, such as the circadian rhythms that are phase delayed and advanced by light given at early and late subjective night, respectively. Despite the importance of the phase-dependent light responses, little is known about the underlying molecular mechanism. We performed a comprehensive analysis of genes induced by light in a phase-dependent manner in the chicken pineal gland, an organ that represents a unique vertebrate clock system harboring intrinsic light sensitivity. Newborn chicks were entrained to 12-h light/12-h dark cycle for 7 days then transferred to constant darkness for a day to be exposed to light for 1 h from CT (circadian time) 6 (representing subjective day), CT14 (early subjective night) or CT22 (late subjective night). Control animals were kept in the dark without light pulse. The pineal glands were isolated at the end of the 1-h light pulse for gene expression analysis by Affymetrix GeneChip. Each condition contains 2 biological samples.
2011-03-08 | E-GEOD-21915 | biostudies-arrayexpress
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