Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional response of A. thaliana Root and Shoot tissue to light stress and presence of microbial communities

ABSTRACT: Transcriptional response of A. thaliana Root and Shoot tissue to light stress and presence of microbial communities

PROVIDER: PRJNA671859 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12898856.fastq.gz	Fastqsanger.gz
	SRR12898857.fastq.gz	Fastqsanger.gz
	SRR12898858.fastq.gz	Fastqsanger.gz
	SRR12898859.fastq.gz	Fastqsanger.gz
	SRR12898860.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Transcriptional response of A. thaliana Root and Shoot tissue to light stress and presence of microbial communities

Project description:We profiled the root and shoot transcriptomes of BFO-colonized (Bacteria, Fungi, Oomycetes) and germ free A. thaliana exposed to Low PAR (photoactive radiation, LP) and normal condition (NC) in the gnotobiotic FlowPot system five weeks post inoculation.

2020-10-27 | GSE160106 | GEO

Transcriptional response of A. thaliana Root and Shoot tissue to light stress and presence of microbial communities in myc2-3 and MYC2-Flag lines

Project description:MYC2 is a central node controlling the crosstalk between JA and other phytohormone signalling pathways and regulating responses to light and circadian clock. We hypothesized that this transcription factor might coordinate prioritization of microbiota-induced growth over defense under suboptimal light conditions

2020-10-27 | GSE160115 | GEO

ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana

Project description:Injured plant somatic tissues regenerate themselves by establishing the shoot or root meristems. In Arabidopsis (Arabidopsis thaliana) a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, it remains elusive whether and how the environmental factors influence this process. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyl as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of the HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristem through the regulatory network governed by HY5, thus, highlighting the influence of light signals on plant developmental plasticity.

2024-09-16 | GSE236147 | GEO

Transcriptional response of A. thaliana Root and Shoot tissue to light stress and presence of microbial communities in myc2-3 and MYC2-Flag lines

Project description:Transcriptional response of A. thaliana Root and Shoot tissue to light stress and presence of microbial communities in myc2-3 and MYC2-Flag lines

| PRJNA671872 | ENA

Root development and responses are alerted by light

Project description:Investigation of whole genome gene expression level changes in Arabidopsis roots by the effect of light. Plant growth is sustained by a continuous cell division in meristems followed by cell differentiation and elongation. We have found that in Arabidopsis thaliana roots, flavonols play a key role in regulating the transition from cell division to differentiation. Using an engineered device to grow roots in darkness, but shoot in light cycle, coupled with transcriptomic and metabolomics analysis, we deciphered that flavonols accumulation regulates proliferation-promoting levels of auxin-PLETHORA and superoxide anion (O2-). High flavonols levels restrict auxin transport and the PLETHORA gradient but also superoxide radical content, promoting an accelerated cell differentiation. Furthermore, cytokinin-SHY2 and H2O2-UPB1 pathways, which promote differentiation and, respectively, antagonize auxin and O2- activity, increase flavonols biosynthesis establishing mutual interactions among these pathways. Flavonols function as positional signals integrating hormonal and ROS pathways to determine final organ growth. This work analyze the effect of root illumination in gene transcription. Details of how plants and roots are grown are described in Silva et al. (submitted) A six chip study using total RNA extracted from three independent experiments of Arabidopsis roots growing in presence of light and three independent experiments of Arabidopsis roots growing without light.

2016-04-01 | E-GEOD-68093 | biostudies-arrayexpress

ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana

Project description:ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana

| PRJNA989138 | ENA

Identification of root transcriptional responses to shoot illumination in Arabidopsis thaliana

Project description:This experiment aimed to investigate which genes are involved in the early photomorphogenic root development of dark grown roots when only the shoot was exposed to light.

2019-09-25 | GSE132249 | GEO

Root development and responses are alerted by light

2016-04-01 | GSE68093 | GEO

Plant growth in Arabidopsis is assisted by whole soil microbial communities

Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments. Four samples were analysed in total. One corresponded to a pooled sample of RNA extracted from root tissues of 60 plants. The other three were biological replicates from shoot tissues, each of which contained 20 plants. Controls were used as reference and corresponded to tissues of plants grown in sterile conditions.

2013-03-09 | E-GEOD-44984 | biostudies-arrayexpress

Root-shoot mineral transport as a key target processes involved in Arabidopsis responsiveness to elevated [CO2] conditions

Project description:In this study we explain the physiological, biochemical and gene expression mechanisms adopted by nitrate-fed Arabidopsis thaliana plants growing under elevated [CO2], highlighting the importance of root-to-shoot interactions in these responses The transcriptomic approach (conducted at the root and shoot level) revealed that exposure to 800 ppm [CO2] conditioned the expression of genes involved in the transport of nitrate and mineral elements.

2017-01-01 | GSE64694 | GEO

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