Study of Gene expression under no salt condition from total leaf RNA and Gene expression after five days of salt stress in 150mM NaCl from total leaf RNA
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ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE122850 | GEO | 2019/11/01
REPOSITORIES: GEO
Similar Datasets
Project description:Study of Gene expression under no salt condition from total leaf RNA and Gene expression after five days of salt stress in 150mM NaCl from total leaf RNA
| PRJNA506683 | ENA
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. Wild type Arabidopsis Col-0 plants were grown hydroponically and treated with or without 150mM NaCl and harvested after 4 days of treatment.
2014-06-01 | E-GEOD-53308 | biostudies-arrayexpress
Project description:Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melangena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were subjected to salt stress. The stress applied was 150mM NaCl and control plants were watered without the additional salt. Samples were collected at 0, 6, 12, 24, 48 and 96 hours after the first application of the salt. RNA was isolated using Qiagen RNeasy. Keywords: Direct comparison
2008-02-13 | GSE8158 | GEO
Project description:The salt glands in the epidermis of recretohalophytes play a pivotal role in salt tolerance by secreting excess salts from tissues. Irrespective of the importance of understanding the secretion process, nothing is known about the molecular mechanisms of salt gland development. Limonium bicolor possesses multi-cellular salt glands in the epidermis and provides a model to study salt gland development. We applied next-generation sequencing to profile early leaf development using five distinctly different developmental stages, which were quantified by successive collections of the first true leaf of L. bicolor with precise spatial and temporal resolution. Twenty-two percent of the genes were differentially expressed along the developmental gradient. Cluster analysis revealed specific expression patterns at one stage, and identified enriched functions specific for each developmental stage. Seventy-two genes were identified as highly involved in salt gland differentiation. Salt glands have high homology with trichomes, which was also confirmed by mutants with increased salt gland densities. A model is proposed to illustrate genes participating in salt gland differentiation. This unique dataset lays the foundation for identifying key genes involved in salt gland development and salt secretion, which is a requisite for understanding mechanisms that could make agriculture possible in saline areas worldwide.
2016-11-18 | GSE52549 | GEO
Project description:To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.
2019-06-19 | GSE109617 | GEO
Project description:To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.
2019-06-19 | GSE109616 | GEO
Project description:Salt stress is a rising threat to agriculture system. The accumulation of salts near the plant roots hampers the normal uptake of water causing osmotic stress and ionic toxicity to the plant. Thompson Seedless is a popular table grape variety of Vitis vinifera L., which is sensitive to salt stress when grown on its own roots; grafting it onto a wild rootstock such as 110 Richtor (110R) makes it tolerant to salt stress. In the present study, shotgun-proteomics approach was used for the investigation of salt stress induced molecular response of own rooted and 110R grafted Thompson Seedless grapevines. A salt stress experiment was conducted on sixteen month old potted grapevines. The grapevines were treated with 150mM NaCl solution for seven days and the control vines were irrigated with tap water. The young leaf samples were collected from control and treated vines at three time-points viz. 6 hours, 48 hours and 7 days of salt stress. The stress responsive proteins identified through statistical analysis revealed a distinct response to salinity in both the vines.
2020-01-27 | PXD015515 | Pride
Project description:Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines.
2021-12-20 | GSE167342 | GEO
Project description:Purpose: Genome-wide expression analysis for introgression line 9L136 and indica variety 93-11 under salt reatment and control to identify specifically differentially expressed in 9L136 under salt stress. Methods: Roots of two-half leaf seedlings of 9L136 and 93-11 were sequenced using an Illumina HiSeq2500 Sequencer; high-quality paired-end reads were mapped to the Nipponbare reference genome (MSU Rice Genome Annotation Project Release 7) using the spliced read mapper TopHat version 2.0.12, and Significant differentially expressed genes (DEGs) were determined based on a threshold of 2-fold expression change and false discovery rate (FDR) < 0.05 using Cuffdiff, one module of Cufflinks. qRT-PCR analysis were performed using SYBR Green Master Mix on CFX96 Real Time System. Results: 1388 genes which specifically differentilly expressed in 9L136 under salt stress were identified, and expression profile of 18 genes randomely selected was confirmed by qRT-PCR.
2017-07-22 | GSE101734 | GEO
Project description:We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80mM or 150mM NaCl after digestion contain predominantly mononucleosomes and represent calssical 'active' chromatin. Profiles of these low-salt-soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of RNA polymerase II. Nearly quantitative recovery of chromatin is obtained with 600mM NaCl, however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics. Keywords: Chromatin affinity-purification on microarray For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2008-12-12 | GSE13217 | GEO