Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nannochloropsis data LC-MS/MS - Transcriptomic and proteomic responses to very low CO2 suggest multiple carbon concentrating mechanisms in Nannochloropsis oceanica

ABSTRACT: Analysis of the CO2 pathway under high and low carbon supply in Nannochloropsis oceanica Imet1

OTHER RELATED OMICS DATASETS IN: GSE55861

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Nannochloropsis Oceanica Strain Imet1

SUBMITTER: Mohamed El Hajjami

LAB HEAD: Ansgar Poetsch

PROVIDER: PXD010030 | Pride | 2019-11-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	0823_IMET1_protein_annotationkeratin.fasta	Fasta
	0h1-1.raw	Raw
	0h1-2.raw	Raw
	0h1-3.raw	Raw
	0h1-4.raw	Raw

Items per page:

1 - 5 of 137

Publications

Transcriptomic and proteomic responses to very low CO<sub>2</sub> suggest multiple carbon concentrating mechanisms in <i>Nannochloropsis oceanica</i>.

Wei Li L El Hajjami Mohamed M Shen Chen C You Wuxin W Lu Yandu Y Li Jing J Jing Xiaoyan X Hu Qiang Q Zhou Wenxu W Poetsch Ansgar A Xu Jian J

Biotechnology for biofuels 20190628

<h4>Background</h4>In industrial oleaginous microalgae such as <i>Nannochloropsis</i> spp., the key components of the carbon concentration mechanism (CCM) machineries are poorly defined, and how they are mobilized to facilitate cellular utilization of inorganic carbon remains elusive.<h4>Results</h4>For <i>Nannochloropsis oceanica</i>, to unravel genes specifically induced by CO<sub>2</sub> depletion which are thus potentially underpinning its CCMs, transcriptome, proteome and metabolome profile ...[more]

PMID: 31297156

Similar Datasets

Nannochloropsis data LC-MS/MS for CA mutant and WT

Project description:Analysis of the CO2 pathway under high carbon supply in Nannochloropsis oceanica Imet1 which compares the WT with a generated carboanhydrase 2 knockdown mutant

2022-02-28 | PXD010076 | Pride

300 ppm Citrinin treatment for 2 h (GPL4399)

Project description:The availability of yeast DNA microarrays provides the possibility of monitoring gene expression levels as a function to toxin exposure, and consequently as a means of determining mechanisms of toxicity. This system possesses the benefit of the essential volume of yeast cultures, the high reproducibility of expression profiles, and the massive functional information. Because small amount of biological sample cultures are required for this analysis, toxicity test for rare chemical such as mycotoxins which is a natural compound and difficult to be artificially synthesized. Citrinin [518-75-2], 4,6-dihydro-8-hydroxy-3,4,5-trimethyl-6-oxo-3H-2-benzopyran-7-crboxylic acid, is the one of the popular mycotoxicin produced by Penicillium and Aspergillus family possibly spread all over the world. This natural chemicals is one of the well characterized mycotoxin but the information especially mechanism of toxic action is limited. We used two types of microarrays, one have ORF (Open reading Frame) fragment on the surface of the glass as probes and the other have probes as oligonucleotide probes on the microarray with 3 dimensions. We compared data properties and studied the toxicity of citrinin to yeast cells. Keywords: stress response Biological samples were prepared from 3 independent experiments. Hybridization were done triplicate in each sample-control set. Sample labeling were swapped between 1st hybridization (control = Cy5, sample = Cy3) and 2nd and 3rd hybridization (control = Cy3, sample = Cy5).

2010-06-10 | E-GEOD-6101 | biostudies-arrayexpress

300 ppm Citrinin treatment for 2 h

Project description:This SuperSeries is composed of the following subset Series: GSE6101: 300 ppm Citrinin treatment for 2 h (GPL4399) GSE6111: 300 ppm Citrinin treatment for 2 h (GPL1945) Keywords: SuperSeries Refer to individual Series

2010-06-10 | E-GEOD-6118 | biostudies-arrayexpress

Transcriptomic measurements of Nannochloropsis oceanica CCMP1779 through a light:dark cycle

Project description:Nannochloropsis oceanica CCMP1779 is a marine unicellular stramenopile and an emerging reference species for basic research on oleogenic microalgae with biotechnological relevance. We investigated its physiology and transcriptome under light/dark cycles. We observed oscillations in lipid content and a predominance of cell division in the first half of the dark phase. Globally, more than 60% of the genes cycled in N. oceanica CCMP1779, with gene expression peaking at different times of the day. Interestingly, the phase of expression of genes involved in certain biological processes was conserved across photosynthetic lineages. Furthermore, in agreement with our physiological studies we found the processes of lipid metabolism and cell division enriched in cycling genes. For example, there was tight coordination of genes involved in the lower part of glycolysis, fatty acid synthesis and lipid production at dawn preceding lipid accumulation during the day. Our results suggest that diel lipid storage plays a key role for N. oceanica CCMP1779 growth under natural conditions making this alga a promising model to gain a basic mechanistic understanding of triacylglycerol production in photosynthetic cells. Our data will help the formulation of new hypotheses on the regulation transcriptional control of cell growth and metabolism in Nannochloropsis. Nannochloropsis oceanica CCMP was entrained to 12:12 light:dark cycles and biological replicates collected every 3 hours for a cycle for a total of 16 samples.

2015-08-01 | E-GEOD-69460 | biostudies-arrayexpress

Transcriptomic and proteomic choreography in response to light quality variation reveals metabolic acclimation in marine Nannochloropsis oceanica

Project description:Analysis of the carbon, photosynthesis etc. pathway under normal and red/blue light conditions in Nannochloropsis oceanica Imet1

2021-01-04 | PXD016054 | Pride

300 ppm Citrinin treatment for 2 h (GPL1945)

Project description:The availability of yeast DNA microarrays provides the possibility of monitoring gene expression levels as a function to toxin exposure, and consequently as a means of determining mechanisms of toxicity. This system possesses the benefit of the essential volume of yeast cultures, the high reproducibility of expression profiles, and the massive functional information. Because small amount of biological sample cultures are required for this analysis, toxicity test for rare chemical such as mycotoxins which is a natural compound and difficult to be artificially synthesized. Citrinin [518-75-2], 4,6-dihydro-8-hydroxy-3,4,5-trimethyl-6-oxo-3H-2-benzopyran-7-crboxylic acid, is the one of the popular mycotoxicin produced by Penicillium and Aspergillus family possibly spread all over the world. This natural chemicals is one of the well characterized mycotoxin but the information especially mechanism of toxic action is limited. We used two types of microarrays, one have ORF (Open reading Frame) fragment on the surface of the glass as probes and the other have probes as oligonucleotide probes on the microarray with 3 dimensions. We compared data properties and studied the toxicity of citrinin to yeast cells. Keywords: stress response Series containes 3 hybridization results from independent biological samples, and each experiment have high and low power scanned data respectively.

2010-06-10 | E-GEOD-6111 | biostudies-arrayexpress

Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage

Project description:We investigated soybean seed development because (1) soybean seeds are a major source of food and fuel, (2) soybean seeds have been an excellent system for studying the basic processes controlling seed development for over three decades, and (3) new soybean genomic resources, including the sequence of the soybean genome and the gene expression profiles for all seed compartments, tissues, and cell types, can be used to gain new insights into the regulatory processes required for seed differentiation. We sequenced messenger RNA populations of specific soybean seed compartments, which will provide new insights into gene expression that are important for â??making a soybean seed.â?? Seventeen compartments of the Early Maturation stage of the soybean seeds were analyzed. Three to four biological replicates were collected for each compartment.

2013-04-17 | E-GEOD-46096 | biostudies-arrayexpress

AKT and AMPK site-specific phosphorylation on TBC1D4 biological activity

Project description:TBC1D4 is a 160 kDa multi-domain containing RabGAP (Rab GTPase-activating protein) and a downstream target of the insulin and contraction-activated kinases AKT and AMPK. While phosphorylation of TBC1D4 has been linked to GLUT4 translocation from storage vesicles (GSVs) to the cell surface, its impact on TBC1D4 enzymatic function is not well understood as previous studies mostly investigated the truncated GAP domain lacking the phosphorylation sites. In the present study, we expressed and purified recombinant full-length TBC1D4 using the baculovirus system. Size exclusion chromatography and co-immunoprecipitation experiments revealed that full-length TBC1D4 forms oligomers of ~600 kDa. Moreover, full-length TBC1D4 displayed similar substrate specificity but had a markedly higher specific GAP activity towards Rab10 compared to the truncated GAP domain. Using high-resolution mass spectrometry, we mapped 19 Ser/Thr phosphorylation sites in TBC1D4.

2021-09-10 | PXD024645 | Pride

Microarray analysis of Arabidopsis Col-0 and catalase 2 mutant define interactions between CO2, daylength and H2O2

Project description:Growth daylength, ambient CO2 level, and intracellular hydrogen peroxide (H2O2) availability all impact plant function by modulating signalling pathways, but interactions between them remain unclear. Using a whole-genome transcriptomics approach, we exploited the conditional photorespiratory nature of the catalase-deficient cat2 mutant to identify gene expression patterns responding to these three factors. Arabidopsis Col-0 and cat2 grown for 5 weeks in high CO2 in short days (SD) were transferred to air in SD or long days (LD), and microarray analysis was performed. Of more than 500 genes differentially expressed in Col-0 between high CO2 and transfer to air in SD, the response of about one-third was attenuated by transfer to air in LD. H2O2-responsive genes in cat2 were highly dependent on daylength. The majority of H2O2-induced genes were more strongly up-regulated after transfer to air in SD than to LD, while a smaller number showed an opposing pattern. Responses of other H2O2-dependent genes indicate redox-modulation of the daylength control of fundamental cell processes. The overall analysis provides evidence that (1) CO2 level modulates stress-associated gene expression; (2) both CO2 and H2O2 interact with daylength and photoreceptor signalling pathways; and (3) cellular signalling pathways may be primed to respond to increased H2O2 in a daylength-determined manner. Two genotypes x five conditions experiment, including Arabidopsis Col0WT and cat2-1 plants grown in soil for 5 weeks in a 8h light/16h dark (short day) regime at high CO2 concentration (3000 ppm CO2) and subsequently transferred to air (400 ppm CO2) in a short day or long day (16h light/8h dark) regime for 2 and 4 days. Three biological replicates were used that consist each of a pool of two leaves from different plants. Each sample was hybridized to one Genechip® Arabidopsis ATH1 Genome Array (Affymetrix).

2012-03-07 | E-GEOD-27985 | biostudies-arrayexpress

Targeting the Post-Synaptic Proteome in Alzheimer Disease with Psychosis

Project description:Individuals with Alzheimer Disease who develop psychotic symptoms (AD+P) experience more rapid cognitive decline and have reduced indices of synaptic integrity relative to those without psychosis (AD-P). We sought to determine whether the postsynaptic density (PSD) proteome is altered in AD+P relative to AD-P, analyzing PSDs from dorsolateral prefrontal cortex of AD+P, AD-P, and a reference group of cognitively normal elderly subjects. The PSD proteome of AD+P showed a global shift towards lower levels of all proteins relative to AD-P, enriched for kinases, proteins regulating Rho GTPases, and other regulators of the actin cytoskeleton. We computationally identified potential novel therapies predicted to reverse the PSD protein signature of AD+P. Five days of administration of one of these drugs, the C-C Motif Chemokine Receptor 5 inhibitor, maraviroc, led to a net reversal of the PSD protein signature in adult mice, nominating it as a novel potential treatment for AD+P.

2023-06-19 | PXD042025 | Pride

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