GEO DataSets

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

Type:

Expression profiling by high throughput sequencing

5 related Platforms

37 Samples

Download data: CSV, FASTA

(Submitter supplied) Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effect of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. more...

Organism:

Thalassiosira pseudonana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29842

24 Samples

Download data: CSV

(Submitter supplied) The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom that naturally tolerates a broad range of salinities, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. more...

Organism:

Cyclotella cryptica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32380

27 Samples

Download data: TXT

(Submitter supplied) To identify the molecular components involved in diatom cell division, global transcript level changes were monitored over the silicon-synchronized cell cycle the model diatom Thalassiosira pseudonana.

Organism:

Thalassiosira pseudonana CCMP1335

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16011

20 Samples

Download data: CSV

(Submitter supplied) Enhanced vertical stratification brought about by warming of the ocean surface is expected to reduce vertical circulation and nutrient input with knock-on effects for phytoplankton. Increased nutrient limitation is one predicted outcome, but the response of phytoplankton is uncertain because long-term adaptation to nutrient limitation has not been studied. We used Cu as a model catalytic nutrient to explore the adaptive response of an oceanic diatom to continuous nutrient deprivation. more...

Organism:

Thalassiosira oceanica CCMP1005

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30969

6 Samples

Download data: FASTA, TXT

(Submitter supplied) To test whether elevated CO2 , which drives seawater below pH 7.9, would shift the dynamical expression patterns diatoms in a more natural environment, we designed a controlled mesocosm study at Friday Harbor Laboratories (FHL) Ocean Acidification Environmental Laboratory (OAEL). Briefly, four independent mesocosm tanks were set up with continuous flow (10-12 mL/min) of filtered seawater from the Puget Sound to simulate mid-century (pH 7.9) and acidified oceanic conditions (pH 7.6) in duplicate. more...

Organism:

Thalassiosira pseudonana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29842

16 Samples

Download data: TXT

(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) 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) The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. more...

Organism:

Thalassiosira pseudonana CCMP1335; Thalassiosira pseudonana

Type:

Expression profiling by array

Platform:

GPL22991

30 Samples

Download data: TXT

(Submitter supplied) Purpose:Using Illumina high-throughout sequencing technology, the transcriptome and expression profiles of S. marinoi were sequenced and analyzed. Comprehensive and systematic study of transcriptomic characteristics, analysis of characteristics of Digital Gene Expression Profiling during different growth phase and deep exploration of molecular mechanism for response to the temperature and low silicate stress environment will provide a comprehensive insight into gene expression profiles and provides an important gene resource for future genetic and molecular studies of S. more...

Organism:

Skeletonema marinoi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21394

15 Samples

Download data: FASTA, TXT

(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) Transcriptomic profiling of the diatom Thalassiosira pseudonana at normal and elevated 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.

Organism:

Thalassiosira pseudonana

Type:

Expression profiling by array

Platform:

GPL18682

72 Samples

Download data: TXT

(Submitter supplied) Diatoms are responsible for ~40% of marine primary productivity1, fueling the oceanic carbon cycle and contributing to natural carbon sequestration in the deep ocean2. Diatoms rely on energetically expensive carbon concentrating mechanisms (CCMs) to fix carbon efficiently at modern levels of CO23–5. How diatoms may respond over the short and long-term to rising atmospheric CO2 remains an open question. more...

Organism:

Thalassiosira pseudonana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20057

28 Samples

Download data: CSV, TAB

(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:

Thalassiosira pseudonana CCMP1335; Fragilariopsis cylindrus CCMP1102

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18729 GPL18728

2 Samples

Download data: TAB

(Submitter supplied) Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. more...

Organism:

Pseudo-nitzschia multiseries; Fragilariopsis cylindrus; Thalassiosira pseudonana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18458 GPL18457 GPL18459

27 Samples

Download data: TXT

(Submitter supplied) Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. more...

Organism:

Phaeodactylum tricornutum; Emiliania huxleyi; Micromonas pusilla; Aureococcus anophagefferens; Ostreococcus sp. 'lucimarinus'; Leishmania major; Thalassiosira pseudonana; Cyanidioschyzon merolae; Bathycoccus prasinos; Cryptococcus neoformans var. grubii; Fragilariopsis cylindrus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

12 related Platforms

26 Samples

Download data: GFF, GTF

(Submitter supplied) Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem structure and function in the ocean. Diatoms are an abundant and widespread functional group of phytoplankton that are responsible for significant amounts of primary production in the ocean, however there has not been a comprehensive study of diatom physiological responses to P deficiency. Here, we coupled deep sequencing of transcript tags and quantitative proteomic analysis from the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. more...

Organism:

Thalassiosira pseudonana CCMP1335

Type:

Expression profiling by SAGE

Platform:

GPL13316

2 Samples

Download data

(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