Ontology highlight
ABSTRACT:
PROVIDER: PRJNA594172 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10605341_1.fastq.gz | Fastqsanger.gz | |||
| SRR10605341_2.fastq.gz | Fastqsanger.gz | |||
| SRR10605342_1.fastq.gz | Fastqsanger.gz | |||
| SRR10605342_2.fastq.gz | Fastqsanger.gz | |||
| SRR10605343_1.fastq.gz | Fastqsanger.gz |
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Project description:Poplar (Populus trichocarpa, clone Nisqually-1) plants were grown in a Conviron PGR 15 growth chamber using precise control of temperature, light, and humidity. Diurnal (driven) conditions included 12L:12D light cycles and 25C/12C thermocycles in three different combinations. These were: photocycles (LDHH), 12 hrs. light (L)/12 hrs. dark (D) at a constant temperature (25C; HH); photo/thermocycles (LDHC): 12 hrs. light (L) /12 hrs. dark (D) with a high day temperature (25C) and a low night temperature (12C); and thermocycles (LLHC): continuous light (LL) with 12 hrs. high/12 hrs. low temperature (25C, day; 12C, night). Light intensity and relative humidity were 700 micromol m-2s-2 and 50%, respectively. Three-month-old poplar plants were entrained for at least one week under the respective condition prior to initiation of each experiment. Leaves and stems from individual poplar plants were collected every four hours for 48 hrs in driven (diurnal) conditions followed by a two day freerun spacer under continuous light/temperature followed by two additional days of sampling under the same continuous free run condition.
2010-01-09 | E-MEXP-2509 | biostudies-arrayexpress
Project description:Populus spp. are dedicated woody biomass feedstocks for advanced biofuels and bioproducts. Proper growth and fitness of poplar as a sustainable feedstock depends on timely perception and response to environmental signals (e.g., light, temperature, water). Poplar leaves, like other C3 photosynthesis plants, have evolved oscillating or circadian rhythms that play important roles in synchronizing biological processes with external cues. To characterize this phenomenon at a molecular level, we employed bottom-up proteomics using high-resolution mass spectrometry and de novo-assisted database searching to identify abundance changes in proteins and post-translational modifications in poplar leaf tissue sampled across a 12/12-hour light/dark diurnal period.
2021-05-11 | MSV000087404 | MassIVE
Project description:Microarray technology was used to assess transcriptome changes in poplar (Populus alba L.) under a realistic simulation of increased UV-B radiation. Plants were UV-Bbe (UV-B biologically effective radiation) supplemented with a dose of 6 kJ/m2/day for 12 hours per day and allowed to recover during the night. Poplar plants were UV-B treated using a refined controlled environment able to guarantee a realistic simulation of natural conditions, especially for light parameters such as presence of background UV-B radiation for control plants and balanced PAR/UV-A/UV-B ratio. A time course experiment was planned to look both at the rapid and delayed response of poplar to UVB; two time points after 3 h (T3h) and 30 h (6th hour of the third day of treatment, T30h) were considered. 4 independent biological replicates were analysed for each time point. Competitive hybridisations were carried out using the PICME 28K microarray. Keywords: Time course experiment, stress response
2013-12-01 | GSE9470 | GEO
Project description:Previous studies have shown that a considerable proportion of the Arabidopsis genome cycles under circadian and/or diurnal conditions (Edwards et al., 2006 PMID: 16473970, Blaesing et al., 2005 PMID 16299223). It is likely that the correct phasing of gene expression plays an important role in improving the growth of the model plant (Dodd et al., 2005 PMID: 16040710). A key question is whether similar regulation is occurring in other higher plant species. In this study we measure the diurnal expression pattern of genes in the T89 clone of the hybrid aspen (Populus tremula L. x P. tremuloides Michx.) using the Affymetrix Poplar array. Samples (leaf blades) were taken at 4h intervals over the course of 2 diurnal cycles (18h Light: 6h Dark). Time-points were labelled relative to dawn (time 0) on the first day of sampling. T89 was selected as it has routinely been used for genetic modification since 1992 (Nilsson et al.) and is the genetic background for a large number of transgenic trees created in order to investigate the function of aspen genes, providing potential for genetic manipulations during our further studies. We also measured the diurnal expression pattern of genes in trees with a compromised circadian clock. Trees with less expressed LATE ELONGATED HYPOCOTYL 1 (LHY1) and LHY2 by RNA interference (lhy) line that was created in T89 clone of the aspen hybrid (Populus tremula L. x P. tremuloides Michx.) using the Affymetrix Poplar array. Samples (leaf blades) were taken at 4h intervals over the course of 2 diurnal cycles (18h Light: 6h Dark) as described above. Thus, time-points are labelled relative to dawn (time 0) on the first day of sampling. The data obtained from using a RNAi line in central Clock components complements the study of wild type T89, since they were grown and sampled at the same time under the same conditions.
2018-03-13 | E-MTAB-4516 | biostudies-arrayexpress
Project description:au14-07_clock - llhh clock transcriptome - Correlate clock-controlled diurnal gene expression changes with H2Bub chromatin mark changes on a genome-wide scale. - Wild type seedlings(Col-0)have been grown under Light/Dark conditions(12 h Light:12 h Dark)and thermocycles(23°C day:19°C night).After 10 days of entrainment, the conditions were switched to continuous light and temperature (LLHH) for 2 days. Seedlings have been harvested the 2nd day after the switch at Zeitgeber time 24 and 36 that correspond to dawn and dusk, respectively. llhh clock transcriptome-LLHH clock transcriptome.
2017-02-01 | GSE93340 | GEO
Project description:Microarray technology was used to assess transcriptome changes in poplar (Populus alba L.) under a realistic simulation of increased UV-B radiation. Plants were UV-Bbe (UV-B biologically effective radiation) supplemented with a dose of 6 kJ/m2/day for 12 hours per day and allowed to recover during the night. Poplar plants were UV-B treated using a refined controlled environment able to guarantee a realistic simulation of natural conditions, especially for light parameters such as presence of background UV-B radiation for control plants and balanced PAR/UV-A/UV-B ratio. A time course experiment was planned to look both at the rapid and delayed response of poplar to UVB; two time points after 3 h (T3h) and 30 h (6th hour of the third day of treatment, T30h) were considered. 4 independent biological replicates were analysed for each time point. Competitive hybridisations were carried out using the PICME 28K microarray. Keywords: Time course experiment, stress response Two condition experiment: UVB supplemented plants vs normal UV-B level plants. Biological replicates: 4 UVB suplemented plants, 4 control plants, two time points, one replicate per array. Dye swap between replicates.
2013-12-01 | E-GEOD-9470 | biostudies-arrayexpress
Project description:Plant growth and survival depends to a large extent on the diurnal regulation of cellular processes. Although extensively studied at the transcript level, notably less is known about diurnal fluctuations at the protein level. Here, we report a high-resolution quantitative time-course of the Arabidopsis rosette proteome and phosphoproteome over a 12 h light:12 h dark diel cycle. We monitored the proteome every 2 h and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. Notably, we quantified nearly 5000 proteins and 1800 phosphopeptides, of which 288 and 225, respectively, were found to fluctuate over the time-course. Diurnal proteome and phosphoproteome changes were related to diverse biological processes, including protein translation, light detection, photosynthesis, metabolism and transport. Together, these datasets represent the most comprehensive proteomic analysis of Arabidopsis rosettes to date, allowing us to make multi-level inferences about the diurnal regulation of key cellular plant processes plants.
2020-12-18 | PXD007600 | Pride
Project description:Mammalian and fish pineals play a key role in adapting behaviour to the ambient light conditions through the release of melatonin. In mice, light inhibits nocturnal locomotor activity via the nonvisual photoreceptor Melanopsin. In contrast to the extensively studied function of Melanopsin in the indirect regulation of the rodent pineal, its role in the intrinsically photosensitive zebrafish pineal has not been elucidated. Therefore, it is not evident if the light signalling mechanism is conserved between distant vertebrates, and how Melanopsin could affect diurnal behaviour. A double knockout of melanopsins (opn4.1-opn4xb) was generated in the diurnal zebrafish, which manifests attenuated locomotor activity during the wake state. Transcriptome sequencing gave insight into pathways downstream of Melanopsin, implying that sustained repression of the melatonin pathway is required to elevate locomotor activity during the diurnal wake state. Moreover, we show that light induces locomotor activity during the diurnal wake state in an intensity-dependent manner. These observations suggest a common Melanopsin-driven mechanism between zebrafish and mammals, while the diurnal and nocturnal chronotypes are inversely regulated downstream of melatonin.
2021-12-06 | GSE189906 | GEO
Project description:Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.
2011-03-24 | GSE28124 | GEO
Project description:Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice. we generate rice diurnal gene expression profiles of seedling leaves and flag leaves using 57K Affymetrix rice whole genome array. keywords: rice (Oryza sativa L.), seedling leaves, flag leaves, diurnal, molecular functions, microarray
2011-03-24 | E-GEOD-28124 | biostudies-arrayexpress