Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling by high throughput sequencing of Arabidopsis seedling root and shoot with or without mild transient salt treatment - ARAPORT dataset

ABSTRACT: A relationship between transcript level and histone modifications is apparent in steady state but their dynamic relationship remains to be understood. In this study we used RNA-sequencing to determine transcript levels in Arabidopsis thaliana plants after a short, mild salt treatment at seedling stage (ﾓpriming treatmentﾔ: 50 mM NaCl for 24 hours). The obtained dataset was compared with genome-wide histone modification landscapes measured in the same plant material (see parallel submission of ChIP-Seq data in ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1663).

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Anna Amtmann

PROVIDER: E-MTAB-1668 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome.

Sani Emanuela E Herzyk Pawel P Perrella Giorgio G Colot Vincent V Amtmann Anna A

Genome biology 20130614 6

<h4>Background</h4>In arid and semi-arid environments, drought and soil salinity usually occur at the beginning and end of a plant's life cycle, offering a natural opportunity for the priming of young plants to enhance stress tolerance in mature plants. Chromatin marks, such as histone modifications, provide a potential molecular mechanism for priming plants to environmental stresses, but whether transient exposure of seedlings to hyperosmotic stress leads to chromatin changes that are maintaine ...[more]

PMID: 23767915

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Project description:affy_nitrogen_medicago - affy_nitrogen_medicago - Experiment has been designed to characterize the molecular expression patterns associated to a contrasted modification of the nitrogen status of the whole plant. The systemic effects of nitrogen status modifications are investigated and compared on non nodulated plant supplied with NO3, NH4 or nodulated plants (Sinorhizobium meliloti 2011) supplied with air. The root systems were separated in two compartments of unequal sizes (split root system). Two treatments were applied on the larger compartment in order to modulate the nitrogen status of the plant: for the S treatment, roots are supplied with nutrient solution containing 10 mM NH4NO3,, whereas for the C treatment, roots are supplied with nitrogen free medium. In the case of N2 fixing plants, N limitation was obtained by replacing air by a mixture of Ar and O2 80 per cent and 20 per cent. The effects of these treatments were investigated on roots of the minor compartment supplied continuously with either NO3 1 mM, NH4 1 mM or air (N2) and on the shoots. We were also interested in the molecular expression patterns associated to the roots deprived of N.-The root system of non-nodulated (NO3- and NH4+) or nodulated (N2) plants is split into two unequal parts and each one is installed in a separate compartment. For the S treatement, the major root part is supplied with NH4NO3 10 mM whereas the minor part is supplied with either NO3- 1mM, NH4+ 1mM or N2. For the C treatement, the major root part is supplied with nitrogen-free nutrient solution whereas the minor part is supplied with either NO3- 1mM, NH4plus 1mM or N2. Each treatement is four days long. Samples of roots of six biological types (NO3S, NO3C, NH4S, NH4C, N2S and N2C) were collected. Two biological repeats per biological types have been analyzed. The effect of the S and C treatments were investigated for each N sources by comparing Affymetrix transcriptomes (NO3C vs NO3S, NH4C vs NH4S, N2C vs N2S). Experiment Overall Design: 26 arrays - medicago

Dataset Information

Transcription profiling by high throughput sequencing of Arabidopsis seedling root and shoot with or without mild transient salt treatment - ARAPORT dataset

Publications

Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome.

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