Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcript Profiling of the Aerobic and Anoxic Rice Coleoptile

ABSTRACT: Rice (Oryza sativa L.) seeds can germinate in complete absence of oxygen. Under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. In this series, we compare the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions. Lasanthi-Kudahettige, R, et. al. Plant Physiology (2007). Transcript Profiling of the Anoxic Rice Coleoptile. Keywords: stress response

ORGANISM(S): Oryza sativa

PROVIDER: GSE6908 | GEO | 2007/03/19

SECONDARY ACCESSION(S): PRJNA98521

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice.

Project description:Purpose: To understand the miRNAome changes during coleoptile senescence, small RNA libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. Total RNA was isolated from the harvested tissues. Total four small RNA libraries of coleoptile senescence were constructed and high-throughput sequencing was performed using Illumina GA IIx system . . Results: Small RNA sequencing identified forty-one known and twenty-one novel miRNAs that were differentially expressed during coleoptile senescence. Integration of expression data of transcriptome and miRNAome identified 148 miRNA-mRNA modules, mainly comprised of miRNAs regulating TFs, signaling-associated factors and transporters, thereby demonstrating multi-tiered regulation of coleoptile senescence. Conclusions: The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

2022-07-21 | GSE199238 | GEO

Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice

Project description:Purpose: To understand the transcriptional changes during coleoptile senescence, transcriptome libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. Total RNA was isolated from the harvested tissues. mRNA libraries were generated and sequenced as 101 bp paired-end reads by using Illumina Hiseq 4000. Results: Our analysis revealed that 3166 transcripts were differentially expressed in senescing coleoptile (Day 2) samples as compared to the control. Furthermore, 44 and 273 transcripts showed specific expression in control and day 2 samples, respectively. From the functional category analysis, we observed that 197, 182, 99 and 88 transcripts belonging to signalling, transcription factors, hormone signalling and transporters respectively were differentially expressed during coleoptile senescence . And 15, 12, 3, and 6 transcripts showed senescence specific expression patterns in the transporters, transcription factors, signalling and hormone signalling categories respectively. Conclusions: The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

2022-07-21 | GSE199139 | GEO

Transcriptome profiles of the rice coleoptile of wild type and reduced adh activity (rad) mutant

Project description:Normally, rice can elongate the coleoptile under submerged condition. However, reduced adh activity (rad) mutant cannot elongate the coleoptile under submergence. To investigate the change in gene expression, we performed microarray analysis. In this analysis, we used 1 day old seedling of rice. But it is difficult to isolate only coleoptile from rice embryo without any contamination in this stage. Therefore, we applied laser microdissection (LM) technique to this microarray. By use of LM, we isolated coleoptile from rice embryo and use for microarray analysis. As the results, we found that the differences in the gene expression profiles of coleoptile between wild type and rad mutant.

2011-04-07 | GSE26632 | GEO

Transcriptome profiles of the rice coleoptile of wild type and reduced adh activity (rad) mutant

2011-04-07 | E-GEOD-26632 | biostudies-arrayexpress

Oryza sativa

Project description:Transcript Profiling of the Aerobic and Anoxic Rice Coleoptile

| PRJNA98521 | ENA

Genome-wide transcriptome of the coleoptile and the first leaf treated by white light or shade in rice seedlings

Project description:Purpose: In order to figure out the tissue-specific mechanism in rice, we collected coleoptiles and the first leaves separately from the seedlings treated by 1 hr shade or white light for RNA sequencing.

2016-12-19 | GSE76051 | GEO

Effects of heat, anoxia, and combined heat-anoxia treatments

Project description:Anoxia induces several heat shock proteins and a heat pre-treatment can acclimatize Arabidopsis seedlings to a subsequent anoxic treatment. In this work we analyzed the response of Arabidopsis seedlings to anoxia, heat and a combined heat+anoxia stress. A significant overlapping between the anoxic and heat shock responses has been observed by whole-genome microarray analysis.

2009-05-30 | GSE16222 | GEO

microbial communities from aerobic/anoxic biological filters

Project description:microbial communities from aerobic/anoxic biological filters

| PRJNA504386 | ENA

Quantitative proteomic changes during anoxia and reoxygenation in anoxia-tolerant crucian carp

Project description:The freshwater fish crucian carp (Carassius carassius) can survive complete oxygen depletion (anoxia) for several months at low temperatures, achieved by a combination of reduced energy demand and increased glycolysis fueled by large hepatic glycogen stores. In crucian carp, the energy-requiring protein synthesis is controlled in a tissue-specific manner when oxygen levels decrease. During anoxia, translational rates are maintained at almost normoxic levels in brain, while heart and liver translation rates are strongly reduced. However, little is known about how the global proteome of these tissues are affected by oxygen variations. By applying mass spectrometry-based proteomics, 3304 proteins in brain, 3004 proteins in heart and 2516 proteins in liver were detected, of which 66 brain proteins, 243 cardiac proteins and 162 hepatic proteins were differentially expressed during the course of anoxia-reoxygenation compared to normoxic control. The brain proteome showed few differences in response to oxygen variations, indicating that anoxic survival is not regulated through protein expression in this tissue. Cardiac and hepatic adaptions to anoxia included enrichment of mitochondrial proteins involved in aerobic respiration and mitochondrial membrane integrity. We show that enzymes in the electron transport system (ETS) are regulated in a tissue-specific manner since no ETS components were regulated in brain, but were downregulated in heart and upregulated in liver during anoxia and reoxygenation. Furthermore, complement system activation was enriched in heart during anoxia. During reoxygenation, proteins involved in the cristae junction organization were regulated in the heart, possibly explaining how reactive oxygen species can be avoided when oxygen returns in this master of anoxic survival.

2023-01-27 | PXD032830 | Pride

FNR- vs WT in anoxic conditions

Project description:Salmonella enterica var. Typhimurium (S. Typhimurium) is a Gram-negative, facultative intracellular pathogen that infects the intestinal tracts of humans and animals. In the host, S. Typhimurium encounters a wide range of oxygen concentrations going from oxic conditions in the stomach to near anoxic conditions in the distal sigmoid colon-rectal junction. In Escherichia coli, FNR (Fumarate Nitrate Reductase) is one of the main regulatory proteins involved in oxygen sensing and in controlling the transcription of the genes required for the aerobic/anaerobic transition.. However, the role of FNR in S. Typhimurium is largely unknown. To assess its role in S. Typhimurium, we constructed an FNR- mutant (NC983) in the pathogenic wild-type (WT) strain, ATCC14028s. Keywords: FNR, Salmonella, anaerobic, virulence

2007-01-05 | GSE3657 | 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