GEO DataSets

(Submitter supplied) Anylasis of the diatom Phaeodactylum tricornutum under 64-75-5,Tetracycline hydrochloride stress

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19904

6 Samples

Download data: TXT

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

Organism:

Phaeodactylum tricornutum

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL30913

9 Samples

Download data: BW, TSV

(Submitter supplied) Loss of DNA methylation is traditionally associated with transcriptional up-regulation of transposable elements. Here we describe for the first time expression changes upon loss of DNA methylation in diatoms using Phaeodactylum tricornutum as a model species. The loss of DNA methylation was obtained by generation of DNMT5 KOs, a divergent DNMT with SNF-like domains. Expression analysis confirm the loss of DNA methylation is associated with de-repression of transposable elements in Phaeodactylum tricornutum with indirect effects on protein coding genes.

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30913

6 Samples

Download data: TSV

(Submitter supplied) DNA methylation has been associated with transcriptional repression of transposable elements. Here we describe the first DNA methylation deficient cell line of a diatom by generating DNMT5:KOs in Phaeodactylum tricornutum. These data show the extend of the loss of DNA methylation in DNMT5:KOs compared to the reference strain. All DNA methylation is lost in DNMT5:KOs.

Organism:

Phaeodactylum tricornutum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL30913

3 Samples

Download data: BW

(Submitter supplied) Anylasis of the α-1,3 fucosyltransferase gene function in diatom Phaeodactylum tricornutum

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19904

9 Samples

Download data: TXT

(Submitter supplied) 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. 

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19904

21 Samples

Download data: TXT

(Submitter supplied) Tunicamycin inhibits the first step of protein N-glycosylation modification. However, the physiological, transcriptomic, and N-glycomic effects of tunicamycin on important marine diatom Phaeodactylum tricornutum are still unknown. In this study, comprehensive approaches were used to study the effects. The results showed that cell growth and photosynthesis were significantly inhibited in P. tricornutum under the tunicamycin stress. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19904

6 Samples

Download data: TXT

(Submitter supplied) Purpose: Using RNAseq to profile transcriptomes to compare wildtype and PtTryp2 knockout lines across different nutrient conditions, aim to further explore the molecular function of PtTryp2 in regulating cell growth and responses to N- and P-stress. Methods: Libraries for RNAseq were created from 1µg of mRNA from each culture. The resulting libraries were loaded into the patterned nanoarray, and single-end 50 bp reads were generated on BGIseq500 platform (BGI-Shenzhen, China), with a data output of about 22 M total clean reads for each library. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32251

18 Samples

Download data: RESULTS

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

Organism:

Synechocystis sp. PCC 6803; Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28944 GPL24784

188 Samples

Download data: TXT

(Submitter supplied) 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).

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24784

12 Samples

Download data: TXT

(Submitter supplied) 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).

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24784

104 Samples

Download data: TXT

(Submitter supplied) Atrazine is one of the most commonly used herbicide and has been frequently detected in estuarine and offshore waters worldwide. As a photosystem Ⅱ inhibitor, atrazine may inhibit phytoplankton from fixating of CO2 and alter its carbon metabolism, which will undoubtedly have negative effect on the primary productivity and carbon sequestration capacity of coastal waters. However, the existing reports mainly focused on agriculture and freshwater ecosystems and are mostly toxicity test with high-dose of atrazine, which have little concern about the negative effects of atrazine on the carbon metabolism of phytoplankton and can’t reflect the actual toxic situation in offshore water. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24784

18 Samples

Download data: TXT

(Submitter supplied) Aureochromes represent a unique type of blue-light photoreceptors that possess a blue-light sensing flavin-binding LOV-domain and a DNA-binding bZIP domain. Therefore, in contrast to other photoreceptors, aureochromes are considered as light-driven transcription factors. As a member of the essential group of marine primary producers, the pennate diatom Phaeodactylum tricornutum possesses four aureochromes (PtAUREO1a, 1b, 1c, 2). more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17128 GPL29196

30 Samples

Download data: XLSX

(Submitter supplied) During grazing, damaged cells of various diatom species release oxylipins whose functions include signaling to nearby undamaged cells. Our study focused on the effects of the oxylipin 2-trans, 4-trans-decadienal (DD) during the light cycle on photosynthetic light harvesting complex (LHC) mRNA regulation in Phaeodactylum tricornutum. RNAseq data revealed extensive suppression of LHC mRNAs measured at 3 h while a smaller set of LHC mRNAs were up-regulated. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17128

8 Samples

Download data: TSV

(Submitter supplied) Chromatin organization in Phaeodactylum tricornutum

Organism:

Phaeodactylum tricornutum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19904

3 Samples

Download data: TXT

(Submitter supplied) Photoacclimation of unicellular algae allows for reversible changes in the number and/or effective absorption cross section of photosynthetic units on time scales of hours to days in response to changes in irradiance. The process involves an enigmatic signaling pathway from the plastid to the nucleus.Our results reveal, for the first time, a fundamental pathway of retrograde signal transduction in a eukaryotic photosynthetic alga.

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18499

6 Samples

Download data: TXT

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

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL24762

106 Samples

Download data

(Submitter supplied) Periodic light–dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diel rhythms, the mechanisms regulating these processes are still obscure. By characterizing a Phaeodactylum tricornutum bHLH-PAS nuclear protein, hereby named RITMO1, we shed light on the regulation of the daily life of diatoms. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL24762

53 Samples

Download data: XLSX

(Submitter supplied) Periodic light–dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diel rhythms, the mechanisms regulating these processes are still obscure. By characterizing a Phaeodactylum tricornutum bHLH-PAS nuclear protein, hereby named RITMO1, we shed light on the regulation of the daily life of diatoms. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL24762

53 Samples

Download data: XLSX

(Submitter supplied) 48 h and 72 h after P, transcriptional profiles of P-depleted (-P) and P-replete (+P) cultures depletion were integrated with metabolite and physiological data. It resulted in identification of essential metabolic pathway remodeled under P deficiency. The most significant inductions were related to proteins involved in phosphate acquisition and scavenging, such as phosphate transporters, alkaline phosphatases and nucleotidases. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL7021

12 Samples

Download data: TXT