GEO DataSets

(Submitter supplied) To identify genes involved in the iron-limited stress response and the induction of programmed cell death, gene expression analaysis using whole-genome microarrays was performed on cultures of T. pseudonana growing in replete or iron-limiting conditions Samples were collected at day 3 and day 5 from duplicate cultures; RNA was extracted and microarray analysis was performed

Organism:

Thalassiosira pseudonana

Type:

Expression profiling by array

Platform:

GPL17168

8 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL5690

6 Samples

Download data: GPR

(Submitter supplied) 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. more...

Organism:

Thalassiosira pseudonana CCMP1335; Thalassiosira pseudonana

Type:

Expression profiling by array

Platform:

GPL15414

12 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Thalassiosira pseudonana CCMP1335

Type:

Expression profiling by genome tiling array

Platforms:

GPL6176 GPL6175

30 Samples

Download data: TXT

(Submitter supplied) T. pseudonana tiling arrays were used to validate gene models and to predict new genes in the genome of this diatom. The tiling array data validated transcription of about 41% (4,653) of the 11,390 computationally predicted genes. An additional 1,132 transcripts were identified that did not correspond to modeled genes with few of these transcripts (<17%) predicted to encode proteins with homology (e-value < 10-05) to publicly available proteins. more...

Organism:

Thalassiosira pseudonana CCMP1335

Type:

Expression profiling by genome tiling array

Platform:

GPL6176

2 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Thalassiosira pseudonana CCMP1335

Type:

Expression profiling by array

Platform:

GPL6175

28 Samples

Download data: TXT

(Submitter supplied) We investigated the effects of extracellular silicic acid on the whole Phaeodactylum triconutum transcriptome. In this work, global transcription analyses were combined with comparative studies of other elements, and detailed analyses of the silicon transporters. Our results provide insight on Si-sensing genes and further extend current models for Si uptake. Keywords: Comparative transcriptome analyses from Phaeodactylum triconutum fusiform cells acclimated in a Si-free or silicic acid medium.

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL7021

6 Samples

Download data: GPR, TIFF

(Submitter supplied) Nutrient-starvation induced lipid accumulation has been reported in diverse algae, including diatoms. Molecular mechanisms underlying lipid accumulation in nutrient-starved algae are of interest to inform genetic engineering strategies aimed at improving lipid productivity. Diatom cell walls are made of nanostructured silica which is a unique feature of the group and silicon deprivation induces both growth arrest and lipid accumulation. more...

Organism:

Thalassiosira pseudonana

Type:

Expression profiling by array

Platform:

GPL15414

12 Samples

Download data: CEL

(Submitter supplied) To characterize the transcript level component of metabolic regulation, genome-wide transcript level changes were documented in the model diatom Thalassiosira pseudonana over a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of co-regulated genes as a key feature of global gene regulation in T. more...

Organism:

Thalassiosira pseudonana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17129

14 Samples

Download data: CSV

(Submitter supplied) Iron (Fe) is an important growth limiting factor for diatoms and its availability is further restricted by changes in the carbonate chemistry of the water. We investigated the physiological attributes and transcriptional profiles of the diatom Thalassiosira pseudonana grown on a day:night cycle under different CO2/pH and iron concentrations, that in combination generated available iron (Fe’) concentrations of 1160, 233, 58 and 12 pM. more...

Organism:

Thalassiosira pseudonana CCMP1335

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26653

24 Samples

Download data: TXT, XLSX

(Submitter supplied) In estuaries and coastal areas, salinity regimes vary with river discharge, seawater evaporation, morphology of the coastal waterways, and dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at various time scales, from daily to annual cycling. They might also adapt to physical alteration that might induce loss of connectivity and enclosure of water bodies. Here we integrate physiological-based assays, morphological plasticity with functional genomics approach to examine the regulatory change that occur during the acclimation to salinity in an estuary diatom, Thalassiosira weissflogii. We found that this diatom respond to salinity (i.e. 21, 28 and 35 psu) with minute adjustments of its physiology (i.e., carbon and silicon metabolisms, pigments concentration and photosynthetic parameters). In contrast after short- (~ 5 generations) or long-term (~ 700 generations) culture at the different salinity we found a large transcriptome reprogramming. With most of the genes being down-regulated in long-term, and only a few genes in common between short and long term experiments.

Organism:

Conticribra weissflogii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20284

6 Samples

Download data: FASTA, TSV

(Submitter supplied) Copper (Cu) plays an essential role in cellular metabolism and limits phytoplankton growth and production in parts of the open sea. Whole transcriptome analysis provides a powerful tool to explore gene expression profiles and cellular metabolic pathways regulated by Cu. In this study, we identified Cu-regulated genes by profiling the transcriptomes of an oceanic diatom, Thalassiosira oceanica 1005, adapted to survive in a Cu-limited and Cu-replete environment. more...

Organism:

Thalassiosira oceanica CCMP1005

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28137

9 Samples

Download data: FA, TXT

(Submitter supplied) 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 diatoms’ mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. more...

Organism:

Phaeodactylum tricornutum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13539

3 Samples

Download data: FA

(Submitter supplied) Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to adapt their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL7021

18 Samples

Download data: GPR

(Submitter supplied) Divergent functions of two clades of flavodoxin in diatoms mitigate oxidative stress and iron limitation Thalassiosira pseudonana and 4 open-ocean diatoms were subjected to iron limitation or short-term oxidative stress (hydrogen peroxide). mRNA profiles of T. pseudonana (CCMP1335), Thalassiosira oceanica (CCMP1005), Amphora coffeaeformis (CCMP1405), Chaetoceros sp. (CCMP199), and Cylindrotheca closterium (CCMP340).

Organism:

Thalassiosira oceanica; Amphora coffeiformis; Thalassiosira pseudonana; Chaetoceros sp. CCMP199; Cylindrotheca closterium

Type:

Expression profiling by high throughput sequencing

5 related Platforms

37 Samples

Download data: CSV, FASTA

(Submitter supplied) In summer 2014, we conducted experiments to determine the effects of different N substrates on phytoplankton communities in the North Pacific Ocean and in the transition zone of the California Current and gyre (Shilova, Mills et al., 2017). Samples were incubated with nitrate, ammonium, urea, and filtered deep water (FDW) for 48 hours (T48). Two treatments added iron, alone (Fe) or with a mix of N substrates (N+Fe), to determine the effects of Fe on the utilization of N substrates. more...

Organism:

uncultured marine microorganism

Type:

Expression profiling by array

Platform:

GPL24371

23 Samples

Download data: TXT

(Submitter supplied) Background: Ocean temperatures are projected to increase over the coming century, with dramatic consequences for the marine biosphere. Diatoms are important contributors to marine primary production and the ocean carbon cycle, yet the molecular mechanisms that regulate their acclimation and adaptation to temperature are poorly understood. Method: Here we use a transcriptomic approach to identify the molecular mechanisms associated with temperature acclimation and adaptation in closely related colder- and warmer-adapted diatom species. more...

Organism:

Chaetoceros sp.

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26060

18 Samples

Download data: CSV

(Submitter supplied) The study aims at deciphering the response of Phaeocystis antarctica under iron limitation and iron supplementation at a transcriptomic level.

Organism:

Phaeocystis antarctica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23905

15 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Thalassiosira pseudonana; Thalassiosira pseudonana CCMP1335

Type:

Expression profiling by array

Platform:

GPL16806

19 Samples

Download data: TXT

(Submitter supplied) Background: Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. more...

Organism:

Fragilariopsis cylindrus CCMP1102; Thalassiosira pseudonana CCMP1335

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18729 GPL18728

2 Samples

Download data: TAB