Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Early nutrient starvation response of the diatom Phaeodactylum tricornutum

ABSTRACT: An experiment was performed to determine the similarities on the RNA level between different conditions where cell division stops in the diatom Phaeodactylum tricornutum. Many of these conditions also increase the accumulation of lipids within the cell or impair photosynthesis. The different metabolic responses were evaluated and the dataset was mined for potential transcriptional regulators of these changes. The experimental setup was as follows: Cells from the pennate diatom Phaeodactylum tricornutum were grown in ESAW medium under continous fluorescent light at 21C in baffled shakeflasks. Exponentially growing cells were harvested by centrifugation and washed twice in 21gr/L NaCL to remove nutrients. Cells were subsequently resuspended in the five different media/conditions (control, darkness, no nitrate, no phosphate, nocodazole).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Phaeodactylum tricornutum

SUBMITTER: Plant Systems Biology data submission

PROVIDER: E-MTAB-4096 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom Wild-type Phaeodactylum tricornutum was grown under Fe replete (10,000 nM) and Fe limiting (5nM) conditions. Partial genome gene expression analysis of iron-inducible genes was conducted using a two-color competitive hybridization microarray.

2010-05-27 | E-GEOD-8675 | biostudies-arrayexpress

Analysis of the α-1,3 fucosyltransferase gene funtion in diatom Phaeodactylum tricornutum

Project description:Anylasis of the α-1,3 fucosyltransferase gene function in diatom Phaeodactylum tricornutum

2022-10-03 | GSE214570 | GEO

Anylasis of the diatom Phaeodactylum tricornutum under 64-75-5,Tetracycline hydrochloride stress

Project description:Anylasis of the diatom Phaeodactylum tricornutum under 64-75-5,Tetracycline hydrochloride stress

2023-11-10 | GSE218473 | GEO

Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

Project description:We have done next generation sequencing of optically thin, exponentialy growing Phaeodactylum tricornutum cultures grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation). 3 biologically independent exponentially growing culture of Phaeodactylum tricornutum were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled foro 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis.

2015-01-02 | E-GEOD-56346 | biostudies-arrayexpress

Whole genome McrBC-chip on DNA methylation of diatom Phaeodactylum tricornutum

Project description:Extensive gene methylation correlated strongly with transcriptional silencing and differential expression under specific conditions. DNA methylation and its role in gene regulation is conserved in stramenopile. Methylome of the whole genome of diatom phaeodactylum tricornutum.

2013-06-15 | E-GEOD-47947 | biostudies-arrayexpress

Thermal transcriptome of Phaeodactylum tricornutum in steady-state growth

Project description:Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal acclimation in the model diatom species Phaeodactylum tricornutum by comparing the differential gene expression in cultures acclimated to sub-optimal, optimal, and supra-optimal temperatures (10, 20 and 26.5 °C, respectively).

2021-10-20 | GSE186035 | GEO

Chronic iron limitation induces resistance to ROS

Project description:Diatoms are single celled photosynthetic bloom-forming algae that are responsible for at least 20% of global primary production. Nevertheless, more than 30% of the oceans are considered “ocean deserts” due to iron limitation. We used the diatom Phaeodactylum tricornutum as a model system to explore diatom’s response to iron limitation and its interplay with susceptibility to oxidative stress. By analyzing physiological parameters and proteome profiling, we defined two distinct phases: short-term (< 3 days, phase I) and chronic (> 5 days, phase II) iron limitation. While at phase I no changes in physiological parameters were observed, molecular markers for iron starvation, such as ISIP and flavodoxin, were highly upregulated. At phase II, down regulation of numerous iron-containing proteins was detected in parallel to reduction in growth rate, chlorophyll content, photosynthetic activity, respiration rate and antioxidant capacity. Intriguingly, while application of oxidative stress to phase I and II iron limited cells similarly oxidized the GSH pool, phase II iron limitation exhibited transient resistance to oxidative stress, despite the down regulation of many antioxidant proteins. By comparing proteomic profiles of P. tricornutum under iron limitation and metatranscriptomic data of an iron enrichment experiment conducted in the Pacific Ocean, we propose that iron limited cells in the natural environment resemble the phase II metabolic state. These results provide insights into the trade-off between maximal growth rate and susceptibility to oxidative stress as a possible key determinant in the response of diatoms to iron quota in the marine environment.

2017-01-16 | PXD004694 | Pride

Thermal transcriptome of Phaeodactylum tricornutum in response to gradual heat stress

Project description:Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal stress in the model diatom species Phaeodactylum tricornutum. We expose cultures to high temperature (optimal +8°C) and follow changes in gene expression through time (over a 12 hour period) in comparison to optimal conditions (20 °C).

2021-10-20 | GSE186033 | GEO

Identification and Characterization of MicroRNAs from Phaeodactylum tricornutum by High-throughput Sequencing and Bioinformatics Analysis

Project description:Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatomsâ mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions. A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were differentially expressed in PT1, PT2 and PT3, and their potential targets were involved in various processes. Our results indicated that P. tricornutum contained novel miRNAs that differed from miRNAs of other organisms and that they might play important regulator roles in P. tricornutum metabolism. Constructing and sequencing small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions

2011-08-08 | E-GEOD-29321 | biostudies-arrayexpress

Regulatory mechanism of diurnal fluctuated laminarin in diatom Phaeodactylum tricornutum

Project description:Diatoms played an essential role in marine primary productivity. Polysaccharide chrysolaminarin and neutral lipid, mainly TAG, were necessary carbon fixation in diatom Phaeodactylum tricornutum. Our study speculated on the metabolism pathway of chrysolaminarin, fatty acid, fatty acid β-oxidation and TAG. Transcriptional levels coordinated with carbon fixation metabolism pathway were conjoint analysis in this study.

2022-08-03 | GSE210141 | 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