Single-cell RNA-seq of rice roots grown in gel, non-compacted soil and compacted soil conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE251706 | GEO | 2024/02/01
REPOSITORIES: GEO
Similar Datasets
Project description:Single-cell RNA-seq of rice roots grown in gel, non-compacted soil and compacted soil conditions
| PRJNA1055099 | ENA
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in Col-0 plants grown in soil in response to low temperature over time. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Keywords: time_series_design
2006-08-15 | GSE5535 | GEO
Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated.
2011-02-15 | GSE21213 | GEO
Project description:rs11-07_opine2 - septante soil - Transcriptomic changes induced by opine production in Arabidopsis thaliana grown in natural soil - Arabidopsis thalian Col- line was transformed in order to obtain transgenic lines that produce opine compound (octopine and mannopine). Transgenic lines producing respectively octopine and mannopine and the WT line were grown in greenhouse under long-day condition in pots containing half commercial compost and half soil of la Mérantaise and watered with water. Whole plant aged of one month were harvested and frozen in liquid nitrogen. The plants were ground with a mortar an pestls and RNA extraction was performed with the RNeasy extraction kit (QIAGEN) with cristal of PVP. The RNA concentration was measured on a NANODrop spectrophotometer.
2017-01-05 | GSE93121 | GEO
Project description:Transcriptomic analysis of the cells grown on biphenyl in the sterilized soil and those grown on biphenyl to mid-exponential phase in a liquid medium
2010-06-10 | GSE22240 | GEO
Project description:Transcroptomic analysis of the cells grown on pyruvate in the sterilized soil and those grown on pyruvate to mid-exponenyial phase in a liquid medium
2010-06-10 | GSE22241 | GEO
Project description:Chitin soil amendment is known to improve soil quality, plant growth and plant stress resilience, but the underlying mechanisms are not well understood. In this study, we monitored chitin’s effect on lettuce physiology every two weeks through an eight-week growth period, analyzed the early transcriptional reprogramming and related metabolomic changes of lettuce, in response to crab chitin treatment in peat-based potting soil. In commercial growth conditions, chitin amendment still promoted lettuce growth, increased chlorophyll content, the number of leaves and crop head weight from week six. The flavonoid content in lettuce leaves was altered as well, showing an increase at week two but a decrease from week six. Transcriptomic analysis showed that over 300 genes in lettuce root were significant differentially expressed after chitin soil treatment. Gene Ontology-term (GO) enrichment analysis revealed statistical overrepresentation of GO terms linked to photosynthesis, pigment metabolic process and phenylpropanoid metabolic process. Further analysis of the differentially expressed genes (DEGs) showed that the flavonoid pathway is mostly upregulated whereas the bifurcation of upstream phenylpropanoid pathway towards lignin biosynthesis is mostly downregulated. Metabolomic analysis revealed the upregulation of salicylic acid, chlorogenic acid, ferulic acid, and p-coumaric acid in chitin treated lettuce seedlings. These phenolic compounds mainly influence the phenylpropanoid biosynthesis pathway and may play important roles in plant defense reactions. Our results suggest that chitin soil amendments might activate induced resistance by priming lettuce plants and promote lettuce growth via transcriptional changes.
2023-03-28 | GSE224725 | GEO
Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated. Test animals were exposed to 26 natural soils + 2 control soils. 4 biological replicates per soil containing 25 grams of soil and 30 23-day-old animals per replicate, RNA was isolated after two days of exposure. for the micro-array hybridization design we made use of an interwoven loop design. from the four replicates per soil two were labeled with Cy3 and 2 with Cy5. It was made sure that now two replicates of the same soil were ever hybridized against the same soil.
2011-02-15 | E-GEOD-21213 | biostudies-arrayexpress
Project description:Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.
| S-EPMC4589753 | biostudies-literature
Project description:Temperature is an important ecological condition, and sudden temperature changes in soil can induce stress in soil-dwelling invertebrates. Soil animals can move to more favorable habitats and/or adapt physiologically to a stressful environment. Hyperthermic conditions will impact gene expression as one of the first steps. We use a transcriptomics approach to identify the transcripts of which expression changed in response to heat stress in the springtail Folsomia candida using a 5,131 probe microarray. A temperature shift from 20°C to 30°C for 30 minutes significantly altered the expression of 142 genes, of which 116 were upregulated, and 26 downregulated. Many upregulated genes encoded heat shock proteins (Hsps) or enzymes involved in the synthesis of ATP, such as members of the electron transport chain. Furthermore, genes involved in oxidative stress and anion-transporting ATPases were upregulated. Downregulated were glycoside hydrolases, involved in catalysis of certain disaccharides, which indicate an accumulation of stress-protective disaccharides. The microarray results from this study, which were validated using quantitative RT PCR, reveal a mild response to heat shock in this soil invertebrate, relative to other organisms. This may be due to specific ecological factors during evolution of soil invertebrates, such as the relatively stable temperatures in the soil habitat. This study presents potential candidate genes for future functional studies concerning thermal stress in soil-dwelling invertebrates, like e.g., the investigation of the heat hardening process.
2010-01-16 | GSE17024 | GEO