E-GEOD-67777
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA280870PRJNA280869PRJNA280871
PROVIDER: E-GEOD-67777 | ExpressionAtlas | 2019-05-14
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:We profiled small RNAs obtained from B. cinerea-infected Arabidopsis rosette leaves at four different time points after inoculation.
2014-03-11 | GSE45323 | GEO
Project description:During the senescence stage, leaves undergo degeneration and relocate nutrients accumulated during the growth stage to sink parts such as seeds, critically contributing to plantsâ productivity and fitness. Here, we asked how leaf transcriptome is regulated during the senescence stage by performing directional sequencing of total and small RNAs for the entire lifespan of Arabidopsis leaves. The total RNA and small RNA profiles of the Arabidopsis leaf along lifespan (14 and 7 time points, respectively) were generated by next-generation sequencing using Illumina Hiseq2000. Two independent biological replicates were used for each experiment.
2016-03-16 | E-GEOD-43616 | biostudies-arrayexpress
Project description:ngs2015_01_transition-transition-Identification of transcripts and long non-coding transcripts in wild-type mature rosette leaves of Arabidopsis thaliana during a photoperiodic switch inducing floral transition.-Arabidopsis thaliana Col-0 plants were grown in soil, in growth chamber under white fluorescent light, under short-day (8 hours light/16 hours dark, SD) or long-day (16 hours light/8 hours dark, LD) conditions. Temperature in SD was 21°C during the light period and 18°C during the dark, humidity (65%) remained constant. In LD, temperature (21°C) and humidity (70%) remained constant. Plants were cultured for 4 weeks in individual pot, in SD then transferred in LD. Plants were analysed at different time points before transfer (T0) and after two, three and five days of transfer (T2, T3, T5). The second pair of leaves was collected before dusk, at Zeitgeber time 15 (ZT15) considering ZT 0 the switched on of the light. Three biological replicates were performed. The floral transition occurs between T0 and T5 based on AP1:GUS marker, a inflorescence meristem is not yet visible during this developmental window at the center of the rosette.
2019-04-17 | GSE116123 | GEO
Project description:Nutrient remobilization during leaf senescence nourishes the growing plant. Understanding the regulation of this process is essential for reducing our dependence on nitrogen fertilizers and increasing agricultural sustainability. Our lab is interested in chromatin changes that accompany the transition to leaf senescence. Previously, darker green leaves were reported for Arabidopsis thaliana hac1 mutants, defective in a gene encoding a histone acetyltransferase in the CREB-binding protein family. Here, we show that two Arabidopsis hac1 alleles display delayed age-related developmental senescence, but have normal dark-induced senescence. Using a combination of ChIP-seq for H3K9ac and RNA-seq for gene expression, we identified 44 potential HAC1 targets during age-related developmental senescence. Genetic analysis demonstrated that one of these potential targets, ERF022, is a positive regulator of leaf senescence. ERF022 is regulated additively by HAC1 and MED25, suggesting MED25 may recruit HAC1 to the ERF022 promoter to increase its expression in older leaves.
2019-07-12 | GSE134176 | GEO
Project description:Our study identified long term salt stress treatment to induce symptoms similar to developmental senescence. In order to identify possible crosstalk components shared between developmental and salt-triggered senescence. We first obtained the expression profile of Arabidopsis leaves under the condition of salt-induced senescence (4 days) and then compared it with the transcriptome of developmental leaf senescence.
2014-06-01 | GSE53308 | GEO
Project description:Leaf senescence is an essential developmental process that involves altered regulation of thousands of genes and changes in many metabolic and signaling pathways resulting in massive physiological and structural changes in the leaf. The regulation of senescence is complex and although several senescence regulatory genes have been identified and characterized there is little information on how these individual regulators function globally in the control of the process. In this paper we use microarray analysis to obtain a high-resolution time course profile of gene expression during development of a single leaf over a three week period from just before full expansion to senescence. The multiple time points enable the use of highly informative clustering tools to reveal distinct time points at which signaling and metabolic pathways change during senescence. Analysis of motif enrichment in co-regulated gene clusters identifies clear groups of transcription factors active at different stages of leaf development and senescence. A novel experimental design strategy (A Mead et al, in preparation), based on the principle of the “loop design”, was developed to enable efficient extraction of information about key sample comparisons using a two-colour hybridisation experimental system. With 88 distinct samples (four biological replicates at each of 22 time points) to be compared, the experimental design included 176 two-colour microarray slides, allowing four technical replicates of each sample to be observed. Half of the slides were devoted to assessment of changes in gene expression between time points, using a simple loop design to link 11 samples from either the 7h time points or the 14h time points across the 11 sampling days, directly comparing samples collected on adjacent sampling days (i.e. 19 DAS with 21 DAS, 27 DAS with 29 DAS, etc.), and directly comparing the samples collected at 39 DAS with those collected at 19 DAS. Four separate loops were constructed for the 7h time points and for the 14h time points, using the arbitrary biological replicate labelling to identify the samples to be included in each loop. The remaining slides provided assessment of differences between the 7h and 14h samples and between the arbitrarily labelled biological replicates, with some further assessment of changes between sampling days. All direct comparisons (pairs of samples hybridised together on a slide) were between 7h and 14h samples collected on adjacent sampling days (i.e. 19 DAS with 21 DAS, etc.), including comparisons between samples collected at 39 DAS and at 19 DAS, and different arbitrarily labelled biological replicates. These 88 comparisons formed a single loop connecting all 88 treatments, therefore ensuring that the design was fully connected (allowing each sample to be compared with every other sample).
2011-03-24 | E-GEOD-22982 | biostudies-arrayexpress
Project description:To identify oilseed rape genes with a potential role in N-remobilization during leaf senescence of developmentally old leaves in the lower canopy and young leaves in the upper canopy, transcriptomes of leaf number 4 and leaf number 8 of B. napus (cultivar Mozart) were analysed at different harvest time points under mild N deficiency and optimal N fertilization.
2018-02-01 | GSE97653 | GEO
Project description:Plants adapt to the prevailing photoperiod by optimally adjusting growth and flowering to the availability of energy. When Arabidopsis thaliana plants are grown in long days individual leaf growth is favoured, whereas whole plant leaf area is decreased because of the rapid shift to floral stages and, consequently, the low number of total leaves. To understand the molecular profiles of adaptation to long-day conditions we profiled Arabidopsis leaf number six of plants grown in 16 hours of light at four developmental stages both at the end of the day and the end of the night and compared the profiles to those acquired in short day conditions.
2015-12-14 | PXD000908 | Pride
Project description:The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes.
2015-04-11 | GSE67777 | GEO
Project description:The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes.
2015-04-11 | GSE67776 | GEO