Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next-generation sequence analysis of the submerged Iris tectorum in plant culture and in plant-algae co-culture

ABSTRACT: We conducted a culture experiment by deeply submerging plants in swine wastewater in culturing Iris tectorum and co-culturing Iris tectorum and Dictyosphaerium sp., and found that the plants grew sub-normal in the plant-microalgae co-culture while the plants were dead after 21 days in the plant culture. We generated a comprehensive RNA-seq dataset from the submerged Iris tectorum leaves in both the plant culture and the plant-microalgae co-culture, aiming at providing information on the response mechanisms of the plants to waterlogging stress. Besides raw reads of the RNA-seq dataset, we used DEseq2 algorithms to detect the differently expressed genes in the plants between the different cultures. Additionally, we performed the plant disease resistance gene analysis for all the differentially expressed genes.

ORGANISM(S): Iris tectorum

PROVIDER: GSE122095 | GEO | 2018/11/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Next-generation sequence analysis of the submerged Iris tectorum in plant culture and in plant-algae co-culture

Project description:Next-generation sequence analysis of the submerged Iris tectorum in plant culture and in plant-algae co-culture

| PRJNA503565 | ENA

Project description:RNA seq of submerged iris in swine wastewater: plant culture and co-culture of plant and microalgae

| PRJNA497338 | ENA

Enhanced nitrogen removal via Yarrowia lipolytica-mediated nitrogen and related metabolism of Chlorella pyrenoidosa from wastewater

Project description:To investigate the mechanism by which the microalgae-yeast co-culture system promotes wastewater denitrification. We concluded that microalgae and yeast exhibit a mutually beneficial relationship in the co-culture system. Microalgae nitrogen metabolism can be influenced by both miRNA and mRNA, and the presence of yeast stimulates gene expression in microalgae.

2023-07-12 | GSE231399 | GEO

Non-axenic microalgae culture

Project description:Non-axenic microalgae culture Raw sequence reads

| PRJNA795303 | ENA

miR396e-OsGRF7 module controls rice plant architecture (RNA-Seq)

Project description:Plant-specific growth-regulating factors (GRFs) participate in multiple central developmental processes including root and leaf development, flower and seed formation, plant senescence, and tolerance to stress. While the role of the miRNA-GRFs regulatory module in determining gross morphology, which is one of the most important agronomic traits for crops, have not been comprehensively unraveled yet. Here, we reported that OsGRF7, a target of miR396e and co-activated with OsGIFs, is essential for determining plant architecture in rice. Overexpression of OsGRF7 leads to decreased tiller number, leaf length and leaf angle, reduced plant height and increased grain size, which are mediated by shortened cell length and disordered cell arrangement. Further analyses indicate that OsGRF7 binds the ACRGDA motif in promoters of OsNSP2, OsGASR1 and OsCYP714B1, OsCga1 and OsARF12, which are involved in the synthesis of strigolactones, gibberellins and cytokinins or related to auxin signaling pathway. Our findings establish OsGRF7 as a crucial component in the miR396-OsGRFs/OsGIFs-plant hormone regulatory network that controls rice growth and plant architecture.This dataset records the differential expressed genes between GRF7OE and WT plants.

2020-04-19 | GSE109801 | GEO

Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition

Project description:Phenolic acids (PAs) secreted by donor plants suppress the growth of their susceptible plant neighbours. However, how structurally diverse ensembles of PAs are perceived by plants to mediate interspecific competition remains a mystery. Here, we show that a plant stress granule (SG) marker, RNA-BINDING PROTEIN 47B (RBP47B), is a sensor of PAs in Arabidopsis. PAs including salicylic acid (SA), 4-hydroxybenzoic acid, protocatechuic acid, etc. directly bind RBP47B, promote its phase separation and trigger SG formation accompanied by global translation inhibition. SA-induced global translation inhibition depends on RBP47 family members. RBP47s regulate the proteome rather than the absolute quantity of SG. The rbp47 quadruple mutant shows a reduced sensitivity to the inhibitory effect of the PA mixture as well as to that of PA-rich rice when tested in a co-culturing ecosystem. Our study discovers RBP47B as the long sought-after PA sensor and unveils PA-induced SG formation and translation inhibition as one of the PA perception mechanisms.

2023-08-29 | PXD043123 | Pride

Corn co-culture with Metarhizium

Project description:Metarhizium species were grown in plate (M-100 agar) co-culture with corn, for 4 and 7 days. Plate contents (plant material above hypocotyl removed) were ground under liquid nitrogen and extracted with methanol.

2020-05-10 | MSV000085395 | MassIVE

Metarhizium Co-culture with bean

Project description:Metarhizium species were grown in plate (M-100 agar) co-culture with bean for 4 and 7 days. Plate contents (plant material above hypocotyl removed) were ground under liquid nitrogen and extracted with methanol.

2020-05-10 | MSV000085394 | MassIVE

Bioengineered tumoral microtissues recapitulate desmoplastic reaction of pancreatic cancer

Project description:In this work, we reported a strategy to produce 3D in vitro microtissues of pancreatic ductal adenocarcinoma (PDAC) for studying the desmoplastic reaction activated by the stroma-cancer crosstalk. The purpose of this dataset was to examine the transcriptional expression changes of normal fibroblasts (NF), cancer-associated fibroblasts (CAF) and pancreatic adenocarcinoma cell line (PT45) in 3D versus 2D culture and in mono-culture versus co-culture. Illumina Human BeadChips were used to profile the transcriptome after 12 days of culture. We reported that human PDAC microtissues, obtained by co-culturing PT45 with NF or CAF within biodegradable microcarriers in spinner flask bioreactor, closely recapitulate key PDAC microenvironment characteristics.

2016-12-14 | GSE81850 | GEO

Plants regenerated from tissue culture contain stable epigenome changes in rice

Project description:Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines. We found that all tested transgenic plants had significant losses of methylation compared to untransformed plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability.

2013-03-26 | GSE42410 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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