Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Arabidopsis thaliana seedlings growing axenically, or in the presence of different bacterial Synthetic Community treatments that induced different root morphology

ABSTRACT: This study evaluated the transcriptomic profiles of Arabidopsis thaliana (Col-0) plants grown along four SynCom treatments that induced differential primary root growth. Treatments Dropout Variovorax and DropoutVariovoraxBurkholderia induced primary root growth inhibition (RGI), while treatments Full and DropoutBurkholderia mantained a stereotypical long primary root.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE131156 | GEO | 2019/05/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq of Arabidopsis thaliana seedlings growing in the presence of a bacterial synthetic community under full and low phosphate conditions [PBI]

Project description:This study evaluates the transcriptome of Arabidopsis thaliana seedlings growing in the presence of a 35-member bacterial SynCom under different phosphate availability

2017-03-20 | GSE87338 | GEO

RNA-seq of Arabidopsis thaliana seedlings growing in the presence of a 185-members bacterial synthetic community under full and low phosphate conditions

Project description:This study evaluates the transcriptome of Arabidopsis thaliana seedlings growing in the presence of a 185-member bacterial SynCom under different phosphate availability

2019-04-06 | GSE129395 | GEO

RNA-seq of Arabidopsis thaliana seedlings growing axenically, or in the presence of different bacterial Synthetic Community treatments that induced different root morphology

Project description:RNA-seq of Arabidopsis thaliana seedlings growing axenically, or in the presence of different bacterial Synthetic Community treatments that induced different root morphology

| PRJNA542790 | ENA

Coordination between the microbiota and the root diffusion barriers is required for plant mineral nutrient homeostasis

Project description:RNASeq of roots from two genotypes of Arabidopsis thaliana plants, Col-0 and myb36-2 grown axenically or with a 41 member bacterial Synthetic Community (SynCom) to explore the interaction between the root diffusion barriers and the root microbiome.

2020-11-01 | GSE151376 | GEO

RNA-seq of Arabidopsis thaliana roots exposed to the MAMP flg22 in the presence of a community of commensal bacteria [RST]

Project description:This study evaluates the transcriptome of Arabidopsis thaliana roots exposed to the MAMP flg22 in the presence of a 35-member bacterial SynCom

2021-03-27 | GSE156425 | GEO

Detection of flg22 peptide upon treatment with different Arabidopsis root-derived bacterial supernatant

Project description:Asymptomatic plants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbiota members can activate host innate immunity, which limits pathogen proliferation and curtails plant growth, a phenomenon known as the growth-defense trade-off. We report that in mono-associations, 41% (62/151) of taxonomically diverse root commensals suppress Arabidopsis root growth inhibition (RGI) triggered by immune-stimulating microbe-/damage-associated molecular patterns. 16S rRNA gene amplicon sequencing data reveal that immune activation alters the profile of synthetic communities (SynComs) comprised of RGI non-suppressive strains, while the presence of RGI-suppressive strains attenuates this effect. Chronic root transcriptional outputs in response to colonization with RGI-suppressive or non-suppressive SynComs share a core of genes with a stereotyped expression pattern. However, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Such SynCom-specific modulation of defense is physiologically relevant as mutation of one commensal-downregulated transcription factor, MYB15, or pre-colonization with an RGI-suppressive SynCom render plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that commensals with contrasting MTI modulating capacities interact with the plant host and together buffer the system against pathogen challenge, defense-associated plant growth inhibition and community shift via a crosstalk with the immune system, leading to commensal-host homeostasis.

2021-03-29 | PXD020452 | panorama

RNA-seq of Arabidopsis thaliana seedlings growing in the presence of a bacterial synthetic community under full and low phosphate conditions [PBI_preTreat]

Project description:This study evaluates whether different pre-treatments (+Pi, -Pi and +Phi) influences the phosphate starvation transcriptional response triggered by a bacterial synthetic community in Arabidopsis seedlings.

2017-03-20 | GSE87337 | GEO

Transcriptional response of tea roots of different genotypes to potassium

Project description:Purpose: We investigated root foraging strategies for K of tea plants using a multi-layer split-root system by RNA-seq. Methods: One-year old tea cuttings were cultivated with the roots evenly planted on the two sides of the split root hydroponic box with a root canal. Three treatments were included to simulate the heterogeneous and homogeneous K environments. After 5d treatment, the roots on the two sides of the split root hydroponic box were collected separately and the RNA sequencing were analyzed by the Illumina Hiseq (2500, Illumina, San Diego, CA). Results: RNA-seq data had a linear relationship with qRT–PCR (r2=0.76), which confirmed the reliability of the RNA-seq data. Conclusions: Our study screened the key genes of tea root system to adapt to potassium heterogeneity.

2022-08-17 | GSE198198 | GEO

Effects of Total Dietary Fiber on Cecal Microbial Community and Intestinal Morphology of Growing White Pekin Duck.

Project description:The current study was to investigate the effects of total dietary fiber (TDF) on growth performance, cecal structure, cecal microbial community, and short-chain fatty acids (SCFAs) profiles in the cecum of growing White Pekin ducks. A total of 108 male Pekin ducks of 14-days-old were randomly allocated and fed diets containing 12.4, 14.7, and 16.2% TDF for 35 days. Each dietary treatment consisted of six replicates with six birds each. The results showed that 14.7 and 16.2% TDF treatments promoted growth performance relative to 12.4% TDF treatments (P < 0.05). A total of 14.7 and 16.2% TDF treatments significantly elevated villus height, the ratio of villus height to crypt depth and muscle layer thickness of cecum, and lowered crypt depth compared with 12.4% TDF treatment (P < 0.05). Simultaneously, 14.7 and 16.2% TDF treatments up-regulated Claudin-1 mRNA expression of barrier genes in the cecum compared with 12.4% TDF (P < 0.05). Butyrate-producing bacteria like Oscillopiraceae affiliating to the phyla Firmicutes were observed as a biomarker in the 16.2% TDF. Higher concentration of butyrate in the cecum was obtained in the 14.7% TDF compared with 12.4 and 16.2% TDF (P < 0.05). The concentrations of isobutyrate, valerate, and isovalerate in the cecum were significantly increased in the 16.2% TDF compared with 12.4 and 14.7% TDF (P < 0.05). Meanwhile, the abundance of genus UCG-005 and Enterococcus was positive correlations with isobutyrate and valerate (P < 0.05). However, the concentration of propionate in the cecum significantly decreased in 14.7 and 16.2% TDF treatments relative to 12.4% TDF treatments (P < 0.05). In summary, increasing TDF levels improved growth performance, cecal histomorphology, and barrier function of meat ducks and it might be mediated by the changes of microbiota communities, especially bloom of SCFAs-producing bacteria, which facilitated the interaction between intestinal mucosa and microbiota.

| S-EPMC8440899 | biostudies-literature

The Three-Dimensional Morphology of Growing Dendrites.

Project description:The processes controlling the morphology of dendrites have been of great interest to a wide range of communities, since they are examples of an out-of-equilibrium pattern forming system, there is a clear connection with battery failure processes, and their morphology sets the properties of many metallic alloys. We determine the three-dimensional morphology of free growing metallic dendrites using a novel X-ray tomographic technique that improves the temporal resolution by more than an order of magnitude compared to conventional techniques. These measurements show that the growth morphology of metallic dendrites is surprisingly different from that seen in model systems, the morphology is not self-similar with distance back from the tip, and that this morphology can have an unexpectedly strong influence on solute segregation in castings. These experiments also provide benchmark data that can be used to validate simulations of free dendritic growth.

| S-EPMC4490335 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data