Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA391921 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5756462_1.fastq.gz | Fastqsanger.gz | |||
| SRR5756462_2.fastq.gz | Fastqsanger.gz | |||
| SRR5756463_1.fastq.gz | Fastqsanger.gz | |||
| SRR5756463_2.fastq.gz | Fastqsanger.gz | |||
| SRR5756464_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye
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Project description: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.
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Project description:Next Generation Sequencing Study of Circadian Changes in Transcriptome of Rhesus Macaque Pineal Gland and Retina
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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
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:Pineal function follows a 24-hour schedule, dedicated to the conversion of night and day into a hormonal signal, melatonin. In mammals, 24-hour changes in pineal activity are controlled by a neural pathway that includes the central circadian oscillator in the suprachiasmatic nucleus and the superior cervical ganglia (SCG), which innervate the pineal gland. In this study, we have generated the first next-generation RNA sequencing evidence of neural control of the daily changes in the pineal transcriptome. We found over 3000 pineal transcripts that are differentially expressed (p <0.001) on a night/day basis (70% of these genes increase at night, 376 with fold change >4 or <1/4), the majority of which had not been previously identified as such. Nearly all night/day differences were eliminated by neonatal removal or decentralization of the SCG, confirming the importance of neural input for differential night/day changes in transcript abundance. In contrast, very few non-rhythmic genes showed evidence of changes in expression due to the surgical procedure itself, which is consistent with the hypothesis that post neonatal neural stimulation is not required for cell fate determination and maintenance of phenotype. Many of the transcripts that exhibit marked differential night/day expression exhibited similar changes in response to in vitro treatment with norepinephrine, the SCG neurotransmitter which mediates pineal regulation. Similar changes were also seen following treatment with an analog of the norepinephrine second messenger, cyclic AMP.
2015-09-02 | GSE63309 | GEO
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
Project description:Pineal function follows a 24-hour schedule, dedicated to the conversion of night and day into a hormonal signal, melatonin. In mammals, 24-hour changes in pineal activity are controlled by a neural pathway that includes the central circadian oscillator in the suprachiasmatic nucleus and the superior cervical ganglia (SCG), which innervate the pineal gland. In this study, we have generated the first next-generation RNA sequencing evidence of neural control of the daily changes in the pineal transcriptome. We found over 3000 pineal transcripts that are differentially expressed (p <0.001) on a night/day basis (70% of these genes increase at night, 376 with fold change >4 or <1/4), the majority of which had not been previously identified as such. Nearly all night/day differences were eliminated by neonatal removal or decentralization of the SCG, confirming the importance of neural input for differential night/day changes in transcript abundance. In contrast, very few non-rhythmic genes showed evidence of changes in expression due to the surgical procedure itself, which is consistent with the hypothesis that post neonatal neural stimulation is not required for cell fate determination and maintenance of phenotype. Many of the transcripts that exhibit marked differential night/day expression exhibited similar changes in response to in vitro treatment with norepinephrine, the SCG neurotransmitter which mediates pineal regulation. Similar changes were also seen following treatment with an analog of the norepinephrine second messenger, cyclic AMP. For the in vivo data, there were 8 biological conditions: day and night time points for each of four surgical groups: Control (Ctrl) Sham-surgery (Sham), Decentralized (DCN), and Ganglionectomized (SCGX). Samples were pooled into three biological replicates for each biological condition. For the in vitro data there were 3 biological conditions: Untreated control (CN), DBcAMP-treated (DB), and Norepinephrine-treated (NE). For the pineal enrichment comparison, three samples (i.e. no biological replicates) were used: pineal-day, pineal-night and mixed-tissue. For the mixed tissues sample, the following tissues from three rats sacrificed at ZT7 were used: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland. Total RNA was extracted from each tissue, and then equal amounts of each of the 15 tissues were combined for the final pooled sample.
2015-09-02 | E-GEOD-63309 | biostudies-arrayexpress
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.
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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
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