Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE23916 | GEO | 2010/09/02
SECONDARY ACCESSION(S): PRJNA133181
REPOSITORIES: GEO
Similar Datasets
Project description:Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105K Agilent microarray to investigate diurnal rhythms.
2010-09-02 | GSE23917 | GEO
Project description:Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105K Agilent microarray to investigate diurnal rhythms. The top-most immature ear, 4-5 cm in length, was collected. Plants were sampled every 4 hours over 3 days. Our sampling times were: 6 am (dawn), 10 am, 2 pm, 6 pm, 10 pm and 2 am. Tissues were collected from three field reps and within each field rep we collected samples from three individual plants
2010-09-02 | E-GEOD-23916 | biostudies-arrayexpress
Project description:Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105K Agilent microarray to investigate diurnal rhythms. The top-most fully expanded leaf from each plant collected. Plants were sampled every 4 hours over 3 days. Our sampling times were: 6 am (dawn), 10 am, 2 pm, 6 pm, 10 pm and 2 am. Tissues were collected from three field reps and within each field rep we collected samples from three individual plants
2010-09-02 | E-GEOD-23917 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE23916: Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period GSE23917: Diurnal Regulation of Gene Expression in Leaves Over a 72-Hour Period Refer to individual Series
2010-09-02 | E-GEOD-23918 | biostudies-arrayexpress
Project description:RAW spectrum files associated with "DIURNAL RHYTHMS SPATIALLY AND TEMPORALLY ORGANIZE AUTOPHAGY"
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Project description:Substance use disorders (SUDs) are associated with disruptions in sleep and circadian rhythms that persist during abstinence and may contribute to relapse risk. Repeated use of substances such as psychostimulants and opioids may lead to significant alterations in molecular rhythms in the nucleus accumbens (NAc), a brain region central to reward and motivation. Previous studies have identified rhythm alterations in the transcriptome of the NAc and other brain regions following the administration of psychostimulants or opioids. However, little is known about the impact of substance use on the diurnal rhythms of the proteome in the NAc. We used liquid chromatography coupled to tandem mass spectrometry-based (LC-MS/MS) quantitative proteomics, along with a data-independent acquisition (DIA) analysis pipeline, to investigate the effects of cocaine or morphine administration on diurnal rhythms of proteome in the mouse NAc. Overall, our data reveals cocaine and morphine differentially alters diurnal rhythms of the proteome in the NAc, with largely independent differentially expressed proteins dependent on time-of-day. Pathways enriched from cocaine altered protein rhythms were primarily associated with glucocorticoid signaling and metabolism, whereas morphine was associated with neuroinflammation. Collectively, these findings are the first to characterize the diurnal regulation of the NAc proteome and demonstrate a novel relationship between phase-dependent regulation of protein expression and the differential effects of cocaine and morphine on the NAc proteome.
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Project description:The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). Each of these structures have some overlapping and some distinct functions related to motor control, cognitive processing, motivation, and reward. Previously, we used a “time of death” approach to identify diurnal rhythms in RNA transcripts in human cortical regions. Here, we identify molecular rhythms across the three striatal subregions collected from postmortem human brain tissue in subjects without psychiatric or neurological disorders. Core circadian clock genes are rhythmic across all three regions and show strong phase concordance across regions. However, the putamen contains a much larger number of significantly rhythmic transcripts than the other two regions. Moreover, there are many differences in pathways that are rhythmic across regions. Strikingly, the top rhythmic transcripts in NAc (but not the other regions) are predominantly snoRNAs and lncRNAs, suggesting that a completely different mechanism might be used for the regulation of diurnal rhythms in translation and/or RNA processing in the NAc versus the other regions. Further, although the NAc and putamen are generally in phase with regards to timing of expression rhythms, the NAc and caudate, and caudate and putamen, have several clusters of discordant rhythmic transcripts, suggesting a temporal wave of specific cellular processes with the caudate preceding the other regions. Taken together, these studies reveal distinct transcriptome rhythms across the human striatum and are an important step in helping to understand the normal function of diurnal rhythms in these regions and how disruption could lead to pathology.
2020-12-31 | GSE160521 | GEO
Project description:Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known about the accumulation patterns of proteins. Here, we quantified temporal profiles in the murine hepatic proteome under physiological light–dark conditions using stable isotope labeling by amino acids quantitative MS. To measure the daily accumulation of proteins, we designed an SILAC MS experiment, in which total protein extracts were harvested from C57BL/6J mice every 3 h for 2 d (eight samples per day). Relative protein abundance in each of 16 samples was quantified against a common reference sample labeled using the SILAC method. The generated mass spectra allowed the identification of a total of 5,827 distinct proteins, of which 70% yielded relative measurements in at least 8 of 16 samples. Our analysis identified over 5,000 proteins, of which several hundred showed robust diurnal oscillations with peak phases enriched in the morning and during the night and related to core hepatic physiological functions. Combined mathematical modeling of temporal protein and mRNA profiles indicated that proteins accumulate with reduced amplitudes and significant delays, consistent with protein half-life data. Moreover, a group comprising about one-half of the rhythmic proteins showed no corresponding rhythmic mRNAs, indicating significant translational or posttranslational diurnal control. Such rhythms were highly enriched in secreted proteins accumulating tightly during the night. Also, these rhythms persisted in clock-deficient animals subjected to rhythmic feeding, suggesting that food-related entrainment signals influence rhythms in circulating plasma factors
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