Ontology highlight
ABSTRACT:
PROVIDER: PRJNA749005 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Internal sugar and light specific dependent regulation of leaf gene expression was addressed by changing [CO2] to lower than compensation point [CO2] in combination with light or prolonged darkness. Plants were grown on soil in a 12/12 h light/dark rhythm at 20°C day and night and under normal [CO2]. 5 weeks after germination, the above-ground rosettes of the non-flowering plants were harvested, 12 plants per sample. Plants were harvested 4hrs after the end of night (i) under low (< 50 ppm) [CO2] and 150 µE fluorescent light , (ii) under normal [CO2] and light, and, (iii) under low [CO2] and prolonged darkness. The low [CO2] treatment started 30 min before the end of night and stopped with harvesting. Keywords: repeat
2005-12-01 | GSE3423 | GEO
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:adt07-03_mir398-mutants - mir398 mutant analysis - Defining new targets of miR398 by transcriptome analysis of two miR398 mutant alleles. - Plants were grown on soil in culture chambers under the following conditions, a day/night cycle of 16/8 hours was applied, light intensity was around 100-150 umol m-2 s-1, temperature day/night was 20/15°C. Plants were harvested 17 days later and RNAs were then extracted. The experiment was repeated twice. Keywords: gene knock out
2008-07-11 | GSE10672 | GEO
Project description:Internal sugar and light specific dependent regulation of leaf gene expression was addressed by changing [CO2] to lower than compensation point [CO2] in combination with light or prolonged darkness. Plants were grown on soil in a 12/12 h light/dark rhythm at 20°C day and night and under normal [CO2]. 5 weeks after germination, the above-ground rosettes of the non-flowering plants were harvested, 12 plants per sample. Plants were harvested 4hrs after the end of night (i) under low (< 50 ppm) [CO2] and 150 µE fluorescent light , (ii) under normal [CO2] and light, and, (iii) under low [CO2] and prolonged darkness. The low [CO2] treatment started 30 min before the end of night and stopped with harvesting. Experiment Overall Design: 2 biological replicates of plants under 3 treatments (4hrs low CO2+light, 4hrs low CO2+prolonged darkness, and 4hrs normal CO2+light).
2008-06-12 | E-GEOD-3423 | biostudies-arrayexpress
Project description:We report the results of a genome-wide analysis of AS in Arabidopsis thaliana plants exposed to a 2h light pulse given in the middle of the night, a treatment that simulates the effects of early dawn or late dusk signals. This light affects the plant transcriptome at multiple regulatory layers, and that light regulation of mRNA levels of splicing regulatory factors is likely to mediate light effects on AS contributing to adjust plant physiological processes to the prevailing light environment. Arabidopsis seedlings of the Columbia ecotype were grown under 12 hr light/12 hr dark cycles for 9 days. On the 10th day, half of the plants were exposed to a two-hour pulse of white light given in the middle of the night (ZT18), while the other half were kept in darkness as controls. Both groups of plants were harvested at ZT 20 and light effects on mRNA levels and AS were analyzed through RNA-seq.
2016-08-09 | E-GEOD-68560 | biostudies-arrayexpress
Project description:cea13-01_oxi1 - oxi1 transcriptome - Transcriptomic analysis on the effect of oxi1 mutation under high light stress? - 5 weeks old mutannt (M) and wild type (WT) plants were exposed to high light and low temperature (1300-1350 µmol photons m-2s-1, 7°C/14°C day/night and 380ppm CO2) for 25 hours. ~100 mg fresh weight leaves were harvested, and total RNA prepared from them. For control experiments, leaves were harvested directly from the phytotron (No light stress). Three microarray comparisons were made: Mcontrol/WTcontrol, Mstress/WTstress and Mstress/Mcontrol . For each comparison, 2 biological replicates are performed.
2014-10-01 | GSE61478 | GEO
Project description:adt07-03_mir398-mutants - mir398 mutant analysis - Defining new targets of miR398 by transcriptome analysis of two miR398 mutant alleles. - Plants were grown on soil in culture chambers under the following conditions, a day/night cycle of 16/8 hours was applied, light intensity was around 100-150 umol m-2 s-1, temperature day/night was 20/15°C. Plants were harvested 17 days later and RNAs were then extracted. The experiment was repeated twice. Keywords: gene knock out 4 dye-swap - CATMA arrays
2010-05-25 | E-GEOD-10672 | biostudies-arrayexpress
Project description:Plants are extremely sensitive to and can re-output rhythm by light signals during photoperiod cues. The circadian transcriptome and epigenetically modified rice genome exhibited distinct circadian behavioural outputs under three light signals during the photoperiod.By comparing and analysing the output circadian genes under different light signals, we detected that constant light (LL) shortens the day-night cycle, while constant night (DD) suppresses the oscillation amplitude. The circadian changing lncRNAs at the genome-wide level that were temporally correlated with oscillating genes at proximal loci and accompanied by synchronised circadian oscillations of H3K9ac modifications. We used the Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to profile the open chromatin regions and transcription factor (TF) footprints in rice at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20). The regulation of circadian gene expression occurs, not through temporal regulation of chromatin opening but through time-dependent binding of transcription factors in cis-regulatory elements. We mapped the 4D genome architecture of rice by employing BL-Hi-C, to capture oscillating chromatin interactions at ZT8 and ZT20. Circadian genes within the same peak phases of expression were preferentially coordinated transcription with non-circadian genes. Circadian genes at the ZT8 circadian phase tended to be enriched in ZT8-speific spatial clusters to orchestrate gene expression. Our findings contribute significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways in rice.
2022-09-15 | GSE213090 | GEO
Project description:Plants are extremely sensitive to and can re-output rhythm by light signals during photoperiod cues. The circadian transcriptome and epigenetically modified rice genome exhibited distinct circadian behavioural outputs under three light signals during the photoperiod.By comparing and analysing the output circadian genes under different light signals, we detected that constant light (LL) shortens the day-night cycle, while constant night (DD) suppresses the oscillation amplitude. The circadian changing lncRNAs at the genome-wide level that were temporally correlated with oscillating genes at proximal loci and accompanied by synchronised circadian oscillations of H3K9ac modifications. We used the Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to profile the open chromatin regions and transcription factor (TF) footprints in rice at six time points (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20). The regulation of circadian gene expression occurs, not through temporal regulation of chromatin opening but through time-dependent binding of transcription factors in cis-regulatory elements. We mapped the 4D genome architecture of rice by employing BL-Hi-C, to capture oscillating chromatin interactions at ZT8 and ZT20. Circadian genes within the same peak phases of expression were preferentially coordinated transcription with non-circadian genes. Circadian genes at the ZT8 circadian phase tended to be enriched in ZT8-speific spatial clusters to orchestrate gene expression. Our findings contribute significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways in rice.
2022-09-15 | GSE213089 | GEO