Ectocarpus siliculosus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA43569 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR1166430.fastq.gz | Fastqsanger.gz | |||
| SRR1166441.fastq.gz | Fastqsanger.gz | |||
| SRR1166452.fastq.gz | Fastqsanger.gz | |||
| SRR1166429.fastq.gz | Fastqsanger.gz |
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Project description:Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. The brown algae are also important because they are one of only a very small number of eukaryotic lineages that have evolved complex multicellularity. This work used whole genome tiling array approach to generate a comprehensive transcriptome map of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for the brown algae. Keywords: high-resolution tiling array, brown algae, ectocarpus
2010-04-07 | GSE19912 | GEO
Project description:Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. The brown algae are also important because they are one of only a very small number of eukaryotic lineages that have evolved complex multicellularity. This work used whole genome tiling array approach to generate a comprehensive transcriptome map of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for the brown algae. Keywords: high-resolution tiling array, brown algae, ectocarpus The slides were hybridised with two, labelled samples: 1) a mixture of labelled cDNA corresponding to RNA samples from mature sporophytes and gametophytes and from immature sporophytes stressed either in high salt medium or by addition of hydrogen peroxide and 2) genomic DNA as a control.
2010-04-07 | E-GEOD-19912 | biostudies-arrayexpress
Project description:The pathosystem between the model brown alga Ectocarpus siliculsosus and the oomycete pathogen Eurychasma dicksonii was investigated with the aim to identify proteins involved in host repsonse. Comparative 2D electrophoresis was used to identify protein spots differentially expressed between uninfected control and infected algal tissue.
2018-10-19 | PXD001458 | Pride
Project description:Characterisation of small RNAs in the brown alga Ectocarpus
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Project description:Ectocarpus siliculosus genome sequencing
| PRJNA353612 | ENA
Project description:Ectocarpus siliculosus Raw sequence reads from ddRADseq
| PRJNA371840 | ENA
Project description:A high-resolution transcriptome map of Ectocarpus siliculosus
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Project description:NGS-based mapping of a morphogenetic mutant in the brown alga Ectocarpus siliculosus, by localization of a locus devoid of SNPs in the mutant segregative population.
| PRJEB8207 | ENA
Project description:BackgroundBrown algae are plant multi-cellular organisms occupying most of the world coasts and are essential actors in the constitution of ecological niches at the shoreline. Ectocarpus siliculosus is an emerging model for brown algal research. Its genome has been sequenced, and several tools are being developed to perform analyses at different levels of cell organization, including transcriptomic expression analyses. Several topics, including physiological responses to osmotic stress and to exposure to contaminants and solvents are being studied in order to better understand the adaptive capacity of brown algae to pollution and environmental changes. A series of genes that can be used to normalise expression analyses is required for these studies.ResultsWe monitored the expression of 13 genes under 21 different culture conditions. These included genes encoding proteins and factors involved in protein translation (ribosomal protein 26S, EF1alpha, IF2A, IF4E) and protein degradation (ubiquitin, ubiquitin conjugating enzyme) or folding (cyclophilin), and proteins involved in both the structure of the cytoskeleton (tubulin alpha, actin, actin-related proteins) and its trafficking function (dynein), as well as a protein implicated in carbon metabolism (glucose 6-phosphate dehydrogenase). The stability of their expression level was assessed using the Ct range, and by applying both the geNorm and the Normfinder principles of calculation.ConclusionComparisons of the data obtained with the three methods of calculation indicated that EF1alpha (EF1a) was the best reference gene for normalisation. The normalisation factor should be calculated with at least two genes, alpha tubulin, ubiquitin-conjugating enzyme or actin-related proteins being good partners of EF1a. Our results exclude actin as a good normalisation gene, and, in this, are in agreement with previous studies in other organisms.
| S-EPMC2546422 | biostudies-literature
Project description:The aim of this study was to analyze genome-wide patterns of histone post-translational modifications (PTMs) and nucleosome distribution during the sporophyte and gametophyte generations of the life cycle of the brown alga Ectocarpus. Analysis of the results of this experiment along with those generated by a second experiment “Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, experiment 1” indicated that the histone PTMs H3K4me2, H3K4me3, H3K9ac, H3K14ac and H3K27ac are associated with the transcriptional start sites (TSSs) of actively expressed genes, H3K36me3 preferentially marks gene bodies and is associated with gene activation, H4K20me3 marks transposons and is associated with gene repression, probably through the silencing of transposons in introns. H3K79me2 occurs in zones corresponding to about a third of the genome. These zones often span several genes and genes within H3K79me2 zones exhibit lower levels of transcript abundance.
2020-11-05 | GSE146366 | GEO