Time-course RNA-seq analysis of salt resonse in Arabidopsis and Marchantia
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PROVIDER: PRJNA641427 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: To understand the dynamic salt-sress response in Arabidopsis and Marchantia
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Project description:Purpose: To understand the dynamic salt-sress response in G-prtoein mutants in Arabidopsis and Marchantia
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Project description:We performed a time course analysis (TC data set) of the response of whole seedling roots to 140mM NaCl at 5 time points after transfer (30 minutes, 1, 4, 16 and 32 hours). Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states. While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli. Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis. Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment. We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers. To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types. Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression. Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered. Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context. Keywords: Time course analysis
2008-04-24 | GSE7642 | GEO
Project description:A major limitation in quantitative time-course proteomics is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity, high dynamic samples such as plant extracts, this is tradeoff is especially apparent. To address this, we evaluate multiple composition voltage (CV) High Field Asymetric Waveform Ion Mobility Spectrometry (FAIMSpro) settings using the latest label-free, single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply-quantify the Arabidopsis thaliana seedling proteome at microliter per minute flow rates. Using a micro-flow BoxCar DIA acquisition workflow with -30, -50, -70 CV FAIMSpro settings we are able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-minute gradient, facilitating the analysis of ~48 samples per day. Utilizing this acquisition approach, we next performed an abiotic stress time-course experiment, whereby we quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress. Here, we successfully quantify over >6400 shoot and >8500 root protein groups, respectively, quantifying nearly 9700 unique protein groups total across the study. Collectively, we pioneer a fast-flow, multi-CV FAIMSpro BoxCar DIA acquisition workflow that represents an exciting new analysis approach for quantitative time-course proteomics experimentation in plants.
2024-01-26 | PXD038989 | Pride
Project description:A major limitation in quantitative time-course proteomics is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity, high dynamic samples such as plant extracts, this is tradeoff is especially apparent. To address this, we evaluate multiple composition voltage (CV) High Field Asymetric Waveform Ion Mobility Spectrometry (FAIMSpro) settings using the latest label-free, single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply-quantify the Arabidopsis thaliana seedling proteome at microliter per minute flow rates. Using a micro-flow BoxCar DIA acquisition workflow with -30, -50, -70 CV FAIMSpro settings we are able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-minute gradient, facilitating the analysis of ~48 samples per day. Utilizing this acquisition approach, we next performed an abiotic stress time-course experiment, whereby we quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress. Here, we successfully quantify over >6400 shoot and >8500 root protein groups, respectively, quantifying nearly 9700 unique protein groups total across the study. Collectively, we pioneer a fast-flow, multi-CV FAIMSpro BoxCar DIA acquisition workflow that represents an exciting new analysis approach for quantitative time-course proteomics experimentation in plants.
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Project description:Transcriptional differentiation in response to environmental stresses plays critical roles in adaptation. Mangroves are dominant in intertidal zones and form dense forest at the sea-land interface, but little is known about the impact of transcriptional phenotype on their adaptation to the saline environments. To address this issue, we prepared customized chips containing cDNA from the root cDNA library of a mangrove species, Ceriops tagal, and then monitored the time-course transcript profiles in the roots by conducting a series of microarray experiments. Five durations of salt shock with 500 mM NaCl, namely 2, 5, 10, 24 and 192 hours, were included. A total of 88 unigenes that were recognized to be up- or down-regulated by salt shock and both gene categories in relation to stresses-induced responses and transcription factor activity were over-predominant. The stresses-responsive genes were significantly overrepresented, some of which were regulated in differential manners from their homologues genes in Arabidopsis. Specific transcriptional regulations were employed by C. tagal to cope with salt shock, which could benefit the salt-tolerant lifestyle of this mangrove species and possibly contribute to establishment of adaptation to the saline environments.
2013-12-31 | GSE30909 | GEO
Project description:Transciptome time course of Arabidopsis stigma senescence
| PRJEB24752 | ENA
Project description:We performed a time course analysis (TC data set) of the response of whole seedling roots to 140mM NaCl at 5 time points after transfer (30 minutes, 1, 4, 16 and 32 hours). Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states. While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli. Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis. Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment. We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers. To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types. Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression. Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered. Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context. Experiment Overall Design: Seedlings were grown for 4-5 days before transfer to standard media supplemented with 140 mM NaCl. Whole roots were harvested at 5 time points after the transfer.
2009-04-25 | E-GEOD-7642 | biostudies-arrayexpress
Project description:In this study, we set to take advantage of Marchantias less complex signalling architecture to better understand how plants respond to environmental cues such as stress and time of the day, to modulate the expression of genes and biological pathways. To this end, we constructed an abiotic stress gene expression atlas of Marchantia comprising seven abiotic stresses (darkness, high light, cold, heat, nitrogen deficiency, salt, mannitol) and their pairwise combinations (e.g., cold + salt). We also measured gene expression at six timepoints of a day (12h light/ 12h darkness)
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