Diurnal Variation in Cyanobacterial Communities
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ABSTRACT:
PROVIDER: PRJEB50403 | ENA |
REPOSITORIES: ENA
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Project description:The purpose of this study was to explore diurnal gene expression changes that occur in the RPE/Choroid/Sclera. Mice C57BL/6J were purchased from the Jackson Laboratory (Bar Harbor, ME) and raised to approximately 2 months of age and entrained to a 12hr/12hr light/dark cycle for two weeks. Eye cups from male mice were rapidly dissected and RPE/ choroid/sclera tissues were collected over three consecutive diurnal cycles at Zeitgeber time (ZT) 0.5, 1, 1.5, 4, 11, 13, 16, and 23 hrs, for a total of 24 time points. Three mice were used for each time point and dissections for dark time points were done under dim-red light. To generate a reference RNA for microarray hybridization, whole eyes from equal numbers of male and female mice were collected at ZT6 and ZT7. Time: Samples were collected at the indicated Zeitgeber time points
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Project description:The purpose of this study was to explore diurnal gene expression changes that occur in the RPE/Choroid/Sclera. Mice C57BL/6J were purchased from the Jackson Laboratory (Bar Harbor, ME) and raised to approximately 2 months of age and entrained to a 12hr/12hr light/dark cycle for two weeks. Eye cups from male mice were rapidly dissected and RPE/ choroid/sclera tissues were collected over three consecutive diurnal cycles at Zeitgeber time (ZT) 0.5, 1, 1.5, 4, 11, 13, 16, and 23 hrs, for a total of 24 time points. Three mice were used for each time point and dissections for dark time points were done under dim-red light. To generate a reference RNA for microarray hybridization, whole eyes from equal numbers of male and female mice were collected at ZT6 and ZT7. Time: Samples were collected at the indicated Zeitgeber time points time series design
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Project description:To gain a better understanding of the diurnal variation in gene expression, we analyzed the changes in gene expression in the eye of zebrafish. Dual color oligonucleotide microarrays were used to compare total RNA harvested from eyes of adult zebrafish at midday and midnight. Statistical analyses identified 44 genes which showed significant, 2-fold or more change; 26 genes showed decreased expression at midnight (D/L ≤ 0.5) and 18 genes showed increased expression at midnight (D/L ≥ 2). Seven genes were further analyzed using qPCR. The results of qPCR identified AANAT, Mel1a1, Mel1a3, Mel1b1, Mel1b2 and Melc as genes that showed significant change in expression at dawn, dusk, midday and midnight. These results suggest that expression of melatonin receptors is subject to diurnal regulation. Wild-type ZDR zebrafish (Danio rerio) were obtained from Animal Wonders, San Marcos, TX, and Aquatica Tropicals, Plant City, FL. Fish were conditioned on a 12 hour light/dark cycle for a minimum of 14 days before use. The design of this analysis compared the experimental to the control: midnight samples were used as experimental and midday as control. Samples were collected in triplicate per time point with each replicate representing total RNA pooled from 9 fish. Dual-color microarray was used to compare the midnight and midday samples. A statistically significant (p-value ≤ 0.05) and 2-fold or more change in an experimental sample as compared to a control indicated an up- or down-regulation in gene expression. Supplementary files: In Complete processed data file, "x" marked spots show intensities of less than 1000. In Intensity trimmed data file, all genes with signal intensities of less than 1000 in all triplicate time points were removed from the analysis.
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