Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome and metabolome analysis support that nitrate primarily promotes N and C metabolism in soybean roots and reduces those in nodules.

ABSTRACT: Transcriptome and metabolome analysis support that nitrate primarily promotes N and C metabolism in soybean roots and reduces those in nodules.

PROVIDER: PRJNA413132 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome and metabolome analysis support that nitrate primarily promotes N and C metabolism in soybean roots and reduces those in nodules.

Project description:To dissect differences in gene expression profile of soybean roots and root nodules, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. Nourin No. 2) were inoculated with rhizobia (Bradyrhizobium diazoefficiens USDA110) and were hydroponically cultivated under controlled conditions with nitrogen free culture solution (Saito et al. 2014). At 19 days after planting, each plant were treated with or without 5 mM nitrate for 24 hours. Roots and nodules from three plants were pooled with three biological replications, and total RNA was extracted.

2018-10-01 | GSE104582 | GEO

Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean

Project description:Symbiotic legume nodules and lateral roots arise away from the root meristem via dedifferentiation events. While these organs share some morphological and developmental similarities, whether legume nodules are modified lateral roots is an open question. We dissected emerging nodules (EN), mature nodules (MN), emerging lateral roots (ELR) and young lateral roots (YLR), and constructed strand-specific RNAseq libraries using polyA-enriched RNA preparations. Root sections above and below these organs devoid of any lateral organs were used to construct respective control tissue libraries (ABEN, ABMN, ABELR, ABYLR respectively). High sequence quality, predominant mapping to coding sequences, and consistency between replicates indicated that the RNAseq libraries were of very high quality. We identified genes enriched in emerging nodules, mature nodules, emerging lateral roots and young lateral roots in soybean by comparing global gene expression profiles between each of these organs and adjacent root segments. Potential uses for this high quality transcriptome data set include generation of global gene regulatory networks to identify key regulators; metabolic pathway analyses and comparative analysis of key gene families to discover organ-specific biological processes; and identification of organ-specific alternate spliced transcripts. When combined with other similar datasets especially from leguminous plants these analyses can help answer questions on the evolutionary origins of root nodules and relationships between the development of different plant lateral organs.

2019-04-10 | GSE129509 | GEO

Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules

Project description:Expression data from B. japonicum soybean root nodules including a nodulation time-course experiment with soybean nodules harvested at 10, 13, 21 and 31 dpi and transcriptome of bacteroids formed by a mutant defective in the RNA polymerase transcription factor sigma 54. Two reference data sets were established using B. japonicum cells grown in PSY medium under either aerobic or micro-aerobic conditions. Keywords: genetic modification, time course, growth conditions

2007-07-14 | GSE8478 | GEO

Primarily cultured neurospheres

Project description:Primarily cultured neurospheres

| PRJNA599138 | ENA

Serum microRNA panel to differentiate malignant pulmonary nodules from benign pulmonary nodules

Project description:A serum miRNA combination could be a favourable classifier to differentiate malignant pulmonary nodules from benign pulmonary nodules.

2023-08-27 | GSE157074 | GEO

Transcriptome and Metabolome Analyses Reveal That Nitrate Strongly Promotes Nitrogen and Carbon Metabolism in Soybean Roots, but Tends to Repress It in Nodules.

Project description:Leguminous plants form root nodules with rhizobia that fix atmospheric dinitrogen (N?) for the nitrogen (N) nutrient. Combined nitrogen sources, particular nitrate, severely repress nodule growth and nitrogen fixation activity in soybeans (Glycine max [L.] Merr.). A microarray-based transcriptome analysis and the metabolome analysis were carried out for the roots and nodules of hydroponically grown soybean plants treated with 5 mM of nitrate for 24 h and compared with control without nitrate. Gene expression ratios of nitrate vs. the control were highly enhanced for those probesets related to nitrate transport and assimilation and carbon metabolism in the roots, but much less so in the nodules, except for the nitrate transport and asparagine synthetase. From the metabolome analysis, the concentration ratios of metabolites for the nitrate treatment vs. the control indicated that most of the amino acids, phosphorous-compounds and organic acids in roots were increased about twofold in the roots, whereas in the nodules most of the concentrations of the amino acids, P-compounds and organic acids were decreased while asparagine increased exceptionally. These results may support the hypothesis that nitrate primarily promotes nitrogen and carbon metabolism in the roots, but mainly represses this metabolism in the nodules.

| S-EPMC6027490 | biostudies-literature

Profiling of microglia nodules in multiple sclerosis reveals propensity for lesion formation

Project description:Microglia nodules (HLA-DR+ cell clusters) are associated with brain pathology. In this post-mortem study, we investigated whether they represent the first stage of multiple sclerosis (MS) lesion formation. We show that microglia nodules are associated with more severe MS pathology. Compared to microglia nodules in stroke, those in MS show enhanced expression of genes previously found upregulated in MS lesions. Furthermore, genes associated with lipid metabolism, presence of T and B cells, production of immunoglobulins and cytokines, activation of the complement cascade, and metabolic stress are upregulated in microglia nodules in MS. Compared to stroke, they more frequently phagocytose oxidized phospholipids and possess a more tubular mitochondrial network. Strikingly, in MS, some microglia nodules encapsulate partially demyelinated axons. Taken together, we propose that activation of microglia nodules in MS by cytokines and immunoglobulins, together with phagocytosis of oxidized phospholipids, may lead to a microglia-phenotype prone to MS lesion formation.

2024-01-22 | GSE234700 | GEO

Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean

Project description:Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean

| PRJNA531615 | ENA

Tissue-specific transcriptome analysis in nodules of Lotus japonicus

Project description:Legume plants can establish symbiotic nitrogen fixation (SNF) with rhizobia mostly in root nodules, where rhizobia-infected cells are accompanied with uninfected cells in a mosaic pattern. Inside the mature nodules of legume, carbon and nitrogen nutrients between host plant cells and their resident bacteria are actively exchanged. To elucidate the metabolite dynamics relevant for SNF in nodules, three cell-types from nodule tissues of a model legume, Lotus japonicus, were isolated using laser microdissesction, and transcriptome analysis was done by an oligoarray with 60-mer length representing 21,495 genes. In our cell-type-specific profiling, many genes were identified as being expressed in nodules with spatial-specific manners. Among them, genes coding for metabolic enzymes were classified according to their function, and detailed data analysis figured out that secondary metabolic pathway was highly activated in nodule cortex. In particular, a number of metabolic genes for phenyl propanoid pathway were found as highly expressed genes accompanied with those encoding putative transporters of secondary metabolites. These data suggest the involvement of novel physiological function of phenylpropanoids in SNF.

2011-12-29 | GSE34753 | GEO

Genome wide transcriptome analysis reveals complex regulatory mechanisms underlying phosphate homeostasis in soybean nodules

Project description:Phosphorus (P) deficiency is a major limitation for legume crop production. Although overall adaptations of plant roots to P deficiency have been extensively studied, fragmentary information is available in regards to root nodule responses to P deficiency. In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2,055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of DEGs appeared to be involved in maintaining Pi homeostasis in soybean nodules, including 8 Pi transporters (PTs), 8 proteins containing the SYG1/PHO81/XPR1 domain (SPXs), and 16 purple acid phosphatases (PAPs). The results suggest that a complex transcriptional regulatory network participates in soybean nodule adaption to Pi starvation, most notable a Pi signaling pathway specifically involved in maintaining Pi homeostasis in nodules.

2018-11-20 | GSE116593 | 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