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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Thalassiosira pseudonana exposure to benzopyrene BaP

ABSTRACT: Comparison of transcriptional profile of Thalassiosira pseudonana exposed for 24h to 36.45 ug/L BaP and methanol-treated controls. Four biological replicates (BaP treatment) and six biological replicates (controls).

ORGANISM(S): Thalassiosira pseudonana

SUBMITTER: Teresa Lettieri

PROVIDER: E-MEXP-3558 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptomics responses in marine diatom Thalassiosira pseudonana exposed to the polycyclic aromatic hydrocarbon benzo[a]pyrene.

Carvalho Raquel N RN Bopp Stephanie K SK Lettieri Teresa T

PloS one 20111103 11

Diatoms are unicellular, photosynthetic, eukaryotic algae with a ubiquitous distribution in water environments and they play an important role in the carbon cycle. Molecular or morphological changes in these species under ecological stress conditions are expected to serve as early indicators of toxicity and can point to a global impact on the entire ecosystem. Thalassiosira pseudonana, a marine diatom and the first with a fully sequenced genome has been selected as an aquatic model organism for ...[more]

PMID: 22073232

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Gene profiling of Thalassiosira pseudonana under various growth conditions

Project description:This SuperSeries is composed of the following subset Series: GSE9660: Profiling the transcriptome of Thalassiosira pseudonana under environmentally relevant growth conditions GSE9661: Profiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth Refer to individual Series

2010-05-26 | E-GEOD-9697 | biostudies-arrayexpress

The diatom Thalassiosira pseudonana grown at [normal and elevated CO2] x [normal and elevated light]

Project description:Transcriptomic profiling of the diatom Thalassiosira pseudonana at normal and elevlated CO2 levels and at normal and elevated light levels. Common reference total RNA (Agilent Quick-Amp Cy3-labeled) was used in all arrays as an internal standard. Triplicate batch cultures grown at normal (~400ppm) and elevated (~800ppm) CO2 levels, both at i) normal or ii) elevated light levels. Samples were taken during a) exponential and b) stationary growth during all growth experiments. Result: 48 total transcriptomic measurements: [3 parallel replicates] x [400ppm, 800ppm] x [normal light, high light] x [exponential, stationary] x [2 serial replicates]

2015-11-06 | E-GEOD-57737 | biostudies-arrayexpress

Whole Transcriptome Analysis of the Silicon Response of the Diatom Thalassiosira pseudonana

Project description:Diatom cell walls, made of nanostructured silica, are of interest in diverse areas ranging from cellular structure, to hierarchical organization in biomineralization, to nanotechnology. Thus far, only cell surface proteins and proteins tightly associated with silica matrix have been characterized, and essential components of the silica deposition vesicle (SDV) are unknown, including components of the SDV membrane, cytoskeletal-interacting proteins, and proteins involved in trafficking associated with the SDV. Thus, an understanding of most of the molecular components and the dynamics of cellular processes involved in cell wall synthesis is lacking. In this work we report the first whole-cell response analysis using whole genome microarrays to identify genes potentially involved in diverse aspects of diatom cell division or cell wall synthesis. Thalassiosira pseudonana transcript profiles from precise time points, known to be associated with specific cell wall formation processes in cell-cycle synchronized cultures, suggests that this gene set includes extracellular proteins, silica matrix proteins, and proteins involved in signal transduction, vesicle trafficking, and transport. Protein localization experiments further confirm the first discovery of proteins associated with the SDV membrane. We propose that these proteins provide the interface between extra-SDV organization by the cytoskeleton and intra-SDV organization of silica polymerization determinants, which lead to the higher order organization of diatom silica structure. Analyzed mRNA from 0, 2, 4, 7, 8 and 9 hr of synchronized cell cycle using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as reference point.

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Profiling the transcriptome of Thalassiosira pseudonana under environmentally relevant growth conditions

Project description:T. pseudonana gene-specific arrays were used for differential gene expression. Seven hundred nine genes were differentially expressed by more than 2-fold (Bayesian t-test, p< 0.001) under at least one growth-limiting condition relative to nutrient-replete conditions. A striking result of the hierarchical cluster analysis was the identification of a common set of genes that were upregulated by both iron and silicon limitation, but no other treatment. Together, these two treatments accounted for about one fourth of all differentially expressed genes but almost two thirds of the differentially expressed novel genes, further emphasizing the distinctive aspects of silicon manipulation in diatoms. We analyzed 6 different sets of arrays from 6 growth conditions. Four biological replicates (=4 arrays) were used for each growth condition.

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Diel growth of Thalassiosira pseudonana

Project description:Transcript levels of all T. pseudonana genes was measured every twelve hours throughout the batch (non-chemostatic) growth of axenic cells grown in large glass bioreactors on a 12hr:12hr dark:light cycle for five days. The data were analyzed to reveal the physiological and regulatory changes that recurred in this diatom when transitioning between dark and light conditions, as well as from exponential phase to stationary, nutrient limited conditions. The longitudinal experiment was performed with two replicates, at 400 and 800ppm CO2. Two growth experiments were conducted, with 10 and 9 longitudinal samples collected from each experiment, respectively. Two-color arrays were used with dye flips for labeling. A common internal reference sample was used for one channel on each array. Expression changes for longitudinal analysis were calculated as the difference from the mean log2 expression ratio for each to the common reference sample, for each gene, over all samples within an experiment. For the analysis of diel states in T. pseudonana, samples from the two series were matched according to the time from innoculation, and divided into four classes: dawn samples (taken at the end of each dark phase), dusk samples (taken at the end of each light phase), exponential samples (the first five samples in each series prior to a drop in growth rate on Day 3), and stationary samples (all samples including following the drop in growth rate on Day 3).

2013-04-18 | E-GEOD-45252 | biostudies-arrayexpress

Subcellular proteomics for determining iron limited remodeling of plastids in the model diatom Thalassiosira pseudonana

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