Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1121987 | ENA |
REPOSITORIES: ENA
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Project description:ngs2020_20_ideas-ideas- whole genome (nuclear and organellar) transcriptomic response to a moderate nitrogen starvation-In the IDEAS project, Arabidopsis thaliana Col0 plants were grown on soil from seed for 19 days on the Phenoscope (IJPB, Versailles). The plants were watered with nitrogen-sufficient or nitrogen-limiting solutions. 10 biological replicates were produced. For each sample, 3 rosettes were pooled to extract RNA. The libraries were generated with the Illumina Truseq stranded with ribozero plant leaf and sequenced on a NextSeq500 in single-end 75 bases.
2023-12-01 | GSE234377 | GEO
Project description:This model describes the concept of Cancer Stem Cells(CSC) differentiation and tumor-immune interaction into a generic model that has been validated with known experimental data. Created by COPASI 4.24(Build197)
Abstract:
The tumor microenvironment comprising of the immune cells and cytokines acts as the 'soil' that nourishes a developing tumor. Lack of a comprehensive study of the interactions of this tumor microenvironment with the heterogeneous sub-population of tumor cells that arise from the differentiation of Cancer Stem Cells (CSC), i.e. the 'seed', has limited our understanding of the development of drug resistance and treatment failures in Cancer. Based on this seed and soil hypothesis, for the very first time, we have captured the concept of CSC differentiation and tumor-immune interaction into a generic model that has been validated with known experimental data. Using this model we report that as the CSC differentiation shifts from symmetric to asymmetric pattern, resistant cancer cells start accumulating in the tumor that makes it refractory to therapeutic interventions. Model analyses unveiled the presence of feedback loops that establish the dual role of M2 macrophages in regulating tumor proliferation. The study further revealed oscillations in the tumor sub-populations in the presence of TH1 derived IFN-γ that eliminates CSC; and the role of IL10 feedback in the regulation of TH1/TH2 ratio. These analyses expose important observations that are indicative of Cancer prognosis. Further, the model has been used for testing known treatment protocols to explore the reasons of failure of conventional treatment strategies and propose an improvised protocol that shows promising results in suppressing the proliferation of all the cellular sub-populations of the tumor and restoring a healthy TH1/TH2 ratio that assures better Cancer remission.
2024-09-02 | BIOMD0000000810 | BioModels
Project description:The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning. Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of soil type, soil transplant and landuse changes on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles.
2016-02-04 | GSE77546 | GEO
Project description:The casparian strip serves as a crucial diffusion barrier in the endodermis, playing a vital role in controlling the flow of substances between the root and its external environment. Here, we observed that when the casparian strip is absent, bacteria can accumulate abundantly on the roots. To investigate the impact of this bacterial accumulation on the root indued by casparian strip deficiency , we inoculated Col-0 and sgn3 myb36 roots with CHA0 in a hydroponic system. Ultimately, we found that the bacterial accumulation on the roots, resulting from the absence of the Casparian strip, strongly induces the immune response of the roots. This indicates that the casparian strip plays an important role in regulating the interaction between the root and microorganisms.
2024-11-06 | GSE280679 | GEO
Project description:Bacterial wilt caused by Ralstonia solanacearum is a serious seed/soil borne disease that causes severe yield and quality losses in many plants. In order to understand the change in genome expression of inculated plants, microarray analysis were performed.
2016-11-30 | GSE76071 | GEO
Project description:This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs) affecting host resistance responses. In order to identify an appropriate RIL population to map QTL controlling disease resistance responses, we performed a parental survey of 7 different Arabidopsis accessions. We treated vegetatively grown plants with either salicylic acid or a control solution, and harvested the plants at 3 different time points after chemical treatment. We present Affymetrix GeneChip microarray expression data for 3 biological replications of this parental survey. Experimenter name = Dina St. Clair Experimenter phone = (530) 752-1740 Experimenter department = Department of Plant Sciences Experimenter institute = UC Davis Experimenter address = UC Davis Campus Experimenter address = 114 Amundson Hall Experimenter address = Davis, California Experimenter zip/postal_code = CA Experimenter country = USA Keywords: strain_or_line; compound_treatment; time_series
2007-01-08 | GSE5752 | GEO
Project description:Prunus persica 'Dr. Davis' genome sequencing project
| PRJNA54011 | ENA
Project description:This experiment was donated by The ELP Project website at elp.ucdavis.edu that was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109. The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs) affecting host resistance responses. In order to identify an appropriate RIL population to map QTL controlling disease resistance responses, we performed a parental survey of 7 different Arabidopsis accessions. We treated vegetatively grown plants with either salicylic acid or a control solution, and harvested the plants at 3 different time points after chemical treatment. We present Affymetrix GeneChip microarray expression data for 3 biological replications of this parental survey. Experimenter name = Dina St. Clair; Experimenter phone = (530) 752-1740; Experimenter department = Department of Plant Sciences; Experimenter institute = UC Davis; Experimenter address = UC Davis Campus; Experimenter address = 114 Amundson Hall; Experimenter address = Davis, California; Experimenter zip/postal_code = CA; Experimenter country = USA Experiment Overall Design: 18 samples were used in this experiment
2008-06-14 | E-GEOD-5752 | biostudies-arrayexpress
Project description:Boron is essential for plants, and boron availability in soil is an important determinant of agricultural production. Boron availability in soil is limited at many regions in the world, including Japan. Under boron deficient conditions, leaf expansion and root elongation, apical dominance, flower development,and fruit and seed sets are inhibited. In this work, we analyzed the mRNA expression of genes containing AUGUAA motif in their 5′-UTR, which is induced by boron. We used microarrays to detail the global gene expression underlying boron deficiency in roots.
2013-11-13 | GSE52208 | GEO