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Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, 2020

ABSTRACT: Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, 2020

PROVIDER: PRJNA610257 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11236300.fastq.gz	Fastqsanger.gz
	SRR11236301.fastq.gz	Fastqsanger.gz
	SRR11236302.fastq.gz	Fastqsanger.gz
	SRR11236303.fastq.gz	Fastqsanger.gz
	SRR11236304.fastq.gz	Fastqsanger.gz

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Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, experiment 2

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.

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Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, experiment 1

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 2” 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.

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Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, experiment 2

Project description:Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, experiment 2

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Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, experiment 1

Project description:Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, experiment 1

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Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, 2020

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-11-05 | GSE146369 | GEO

Transcription profiling of Ectocarpus siliculosis sporophytes treated with auxin

Project description:The aim of the experiment is to identify Ectocarpus siliculosus (strain Ec32) genes which are up- or down-regulated by auxin. RNAs were extracted from sporophytes treated with auxin NAA 5.10-6M for 30min or 3h, and labelled either with Cy3 or Cy5. Biological triplicates were performed.

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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 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.

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Analysis of transcript abundances in Ectocarpus life cycle mutants

Project description:The aim of this experiment was to compare transcript abundances in parthenotes (i.e. organisms derived by parthenogenetic development of gametes) of two life cycle mutants of the brown alga Ectocarpus siliculosus with transcript abundances in the wild type sporophyte and gametophyte generations. This is of interest because the two mutations, immediate upright (imm) and ouroboros (oro), cause partial and almost complete hometic conversion, respectively, of the sporophyte into the gametophyte. imm parthenotes exhibit gametophyte-like morphology during early development but remain sporophytes in functional terms (they do not produce gametes) whereas oro parthenotes behave as functional gametophytes and are morphologically indistinguishable from gametophytes apart from the appearance some minor sporophyte-like features very early in development in some individuals. To minimise genetic background effects the samples for this experiment were derived from a segregating population derived from an imm/IMM oro/ORO sporophyte. Four classes of gametophyte were derived from this sporophyte were IMM/ORO (wild type), imm/ORO, IMM/oro and imm/oro. Parthenomes were bulked to provide a wild type sporophyte sample, samples corresponding to the two individual mutants, plus the double mutant. A wild type gametophyte sample was also compared for comparison. Hybridisations with cDNA derived from these five samples were carried out using a NimbleGen expressed-sequence-tag-(EST-)based microarray carrying probes corresponding to 10,600 of the 16,256 genes identified in the Ectocarpus genome.

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Transcription profiling of Ectocarpus strain Esil32 porophyte and gametophyte stages in normal and mutant strains to analyse expression of two sets of genes previously identified as being putatively sporophyte-specific or gametophyte-specific

Project description:The aim of this experiment was to analyse the expression of two sets of genes identified as being putatively sporophyte-specific or gametophyte-specific by a suppressive subtraction hybridisation using cDNA from immature sporophytes and immature gametophytes of the Ectocarpus strain Esil32. The expression of these genes was analysed in the sporophyte and gametophyte generations of the life cycle (again using immature algae that had not yet produces zoidangia) and in the sporophyte generation of a mutant strain, immediate upright, that exhibits gametophyte-like characteristics during the sporophyte generation.

2007-08-01 | E-MEXP-848 | biostudies-arrayexpress

Project description:Ectocarpus siliculosus Sporophytes and Gametophytes Small RNA

| PRJEB2040 | ENA