Arabidopsis Shoot versus Root transcriptome
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE226144 | GEO | 2023/03/05
REPOSITORIES: GEO
Similar Datasets
Project description:Bulk RNA-Seq datasets were generated for the roots and leaves of Pistia stratiotes in order to compare expression of nutrient transporters between the tissues
2023-02-27 | GSE225923 | GEO
Project description:Quinoa is a highly nutritious seudocereal crop that is not well adapted to heat. Improving understanding of quinoa responses to heat would help expand its cultivation to regions with warmer climates. This study profiled gene expression of quinoa plants from accession QQ74 (PI 614886) treated with high tempreatures during anthesis of the main panicle, which lasted 11 days. Heat was applied in four different treatments to profile gene expression changes from root or shoot heating. Treatments were: 1. control with both roots and shoots at 22°C, 2. heated roots with roots at 30°C and shoots at 22°C, 3. heated shoots with roots at 22 °C and shoots at 35°C, and 4. heated roots and shoots with roots at 30°C and shoots at 35°C. Healthy leaves from 3 plants per treatment were sampled from the mid section of the plants, during the first (day 1) and last day (11) of heat treatment, at Zeitgeber time 2. Gene expression of each of the three heat treatments was compared to control using the Kallisto-Sleuth pipeline. These gene expression profiles of quinoa under heat are made available as a community resource to improve understanding of quinoa responses to heat.
2019-07-31 | GSE128155 | GEO
Project description:DNA methylation and nucleosome densities play a critical role in the regulation of gene expression. While much is known about the mechanisms of transcriptional control that are mediated by these, less is known about the degree to which they are tissue-specific. By comparing DNA methylation, nucleosome densities and transcriptional levels in different tissue types we can gain a clearer understanding of the extent to which these mechanisms influence gene expression in a tissue-specific manner. We compared DNA methylation in Arabidopsis shoots and roots and found extensive differences across the genome. We computed DNA methylation differences between roots and shoots at single cytosines and found that one in every 173 cytosines was differentially methylated. In addition, we compared DNA methylation with tissue-specific gene expression and nucleosome density measurements to identify associations between these. We also identified a group of genes that are strongly correlated with these epigenetic marks and are significantly differentially methylated between roots and shoots. These root-specific genes are part of the extensin family, and are preferentially methylated and have at least 10-fold higher expression and lower nucleosome density in roots relative to shoots.
2014-02-11 | GSE52762 | GEO
Project description:Climate change is affecting crop production due to soil salinization and water scarcity, and is predicted to worsen in the coming years. Rice is a major staple food and the most salt-sensitive cereal. High salinity in the soil triggers several adaptive responses in rice to cope with osmotic and ionic stress at the physiological, cellular and molecular levels. A major QTL for salinity tolerance, named Saltol, is present on chromosome 1 of Indian rice landrace varieties such as Pokkali and Nona Bokra. In this study, we characterized the physiological and early proteomic responses to salinity in FL478, an inbred rice line harboring the Saltol region. For this, plantlets were cultured in hydroponic cultures with 100 mM NaCl and evaluated at 6, 24 and 48h. At the physiological level, salinity significantly reduced shoot length after 48 h, whereas root length significantly increased. Moreover, the Na+/K+ ratio was maintained at lower levels in the shoots compared to the roots FL478 plantlets. On the other hand, roots showed a faster and more coordinated proteomic response than shoots, which was evident from only 6h of treatment. These responses were markedly related with transcription- and translation-related proteins. Moreover, roots exhibited a higher accumulation of stress-related proteins in response to salinity treatment, like peroxidase and SalT, which are both present in the Saltol QTL. Both, physiological and proteomic response, showed that roots respond in a highly adaptive manner to salinity stress compared to shoots, which suggests that this tissue is critical to the tolerance observed in varieties harbouring the Saltol region.
2020-12-21 | PXD014669 | Pride
Project description:DNA methylation and nucleosome densities play a critical role in the regulation of gene expression. While much is known about the mechanisms of transcriptional control that are mediated by these, less is known about the degree to which they are tissue-specific. By comparing DNA methylation, nucleosome densities and transcriptional levels in different tissue types we can gain a clearer understanding of the extent to which these mechanisms influence gene expression in a tissue-specific manner. We compared DNA methylation in Arabidopsis shoots and roots and found extensive differences across the genome. We computed DNA methylation differences between roots and shoots at single cytosines and found that one in every 173 cytosines was differentially methylated. In addition, we compared DNA methylation with tissue-specific gene expression and nucleosome density measurements to identify associations between these. We also identified a group of genes that are strongly correlated with these epigenetic marks and are significantly differentially methylated between roots and shoots. These root-specific genes are part of the extensin family, and are preferentially methylated and have at least 10-fold higher expression and lower nucleosome density in roots relative to shoots. No replicates, two libraries for root methylation.
2014-02-11 | E-GEOD-52762 | biostudies-arrayexpress
Project description:Soil salinity presents a notable challenge to agriculture and to increasing the use marginal lands for farming. Here we provide a detailed analysis of the physiology, chemistry and gene expression patterns in roots and shoots of Camelina sativa in response to salt stress. Salt treatment reduced shoot, but not root length. Root and shoot weight were affected by salt, as was photosynthetic capacity. Salt treatment did not alter micro-element concentration in shoots, but increased macro-element (Ca and Mg) levels. Gene expression patterns in shoots indicated that salt stress may have led to shuttling of Na+ from the cytoplasm to the tonoplast and to an increase in K+ and Ca+2 import into the cytoplasm. In roots, gene expression patterns indicated that Na+ was exported from the cytoplasm by the SOS pathway and that K+ was imported in response to salt. Genes encoding proteins involved in chelation and storage were highly up-regulated in shoots, while metal detoxification appeared to involve various export mechanisms in roots. In shoots, genes involved in secondary metabolism leading to lignin, anthocyanin and wax production were up-regulated, probably to improve desiccation tolerance. Partial genome expression partitioning was observed in roots and shoots based on the expression of homeologous genes from the three C. sativa genomes. Genome I and II were involved in the response to salinity stress to about the same degree, while about 10 % more differentially-expressed genes were associated with Genome III. This study has provided valuable information and insight into the response of camelina to salt stress. Examination of this data and comparison to similar studies in more halophytic species will allow development of even more salt-tolerant varieties of this emerging industrial crop.
2017-08-10 | GSE102422 | GEO
Project description:microRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. Phosphate (Pi) is often lacking in natural and agro-climatic environments, and plants have developed strategies to cope with low Pi (LP) availability. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Four small RNA (sRNA) libraries, a mixed degradome cDNA library, and four transcriptomic libraries of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA–target pairs were further validated in the roots and shoots, respectively, using degradome sequencing, including several novel target genes that were cleaved by isomiRNAs with lengths of 18 or 19 nucleotides, which were only differentially expressed in roots. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the “ascorbate and aldarate metabolism” pathway responded to LP, and “circadian rhythm – plant” was specifically enriched in shoots. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. A comparison of transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. Integrated analysis uncovered 14 and 16 miRNA–target pairs that showed negatively correlated expression profiles in roots and shoots, respectively. Moreover, a putative model of miRNA–target interaction involved in plant responses to LP stress is proposed. These results suggest that comprehensive analyses of sRNAs, degradome, and transcriptome provide a useful platform for investigating LP stress in B. luminifera, and may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.
2021-01-13 | GSE138335 | GEO
Project description:microRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. Phosphate (Pi) is often lacking in natural and agro-climatic environments, and plants have developed strategies to cope with low Pi (LP) availability. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Four small RNA (sRNA) libraries, a mixed degradome cDNA library, and four transcriptomic libraries of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA–target pairs were further validated in the roots and shoots, respectively, using degradome sequencing, including several novel target genes that were cleaved by isomiRNAs with lengths of 18 or 19 nucleotides, which were only differentially expressed in roots. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the “ascorbate and aldarate metabolism” pathway responded to LP, and “circadian rhythm – plant” was specifically enriched in shoots. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. A comparison of transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. Integrated analysis uncovered 14 and 16 miRNA–target pairs that showed negatively correlated expression profiles in roots and shoots, respectively. Moreover, a putative model of miRNA–target interaction involved in plant responses to LP stress is proposed. These results suggest that comprehensive analyses of sRNAs, degradome, and transcriptome provide a useful platform for investigating LP stress in B. luminifera, and may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.
2021-01-13 | GSE138334 | GEO
Project description:Comparison of gene expression between shoots of root-wounded seedlings and shoots of control seedlings in Arabidopsis. We identified wounding-induced early (30 min) and late (360 min) root to shoot responsive genes (RtS).
2010-12-31 | GSE26374 | GEO
Project description:RNA was isolated from 23 old barley plants (shoots and roots), line Rolap. PARE libraries were constructed for both barley organs, followed by sequencing of NGS libraries.
2021-02-17 | GSE145423 | GEO