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JaActMedi

ABSTRACT: Actinia mediterranea, genomic and transcriptomic data.

PROVIDER: PRJEB77826 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR13381619.fastq.gz	Fastqsanger.gz
	ERR13765936_1.fastq.gz	Fastqsanger.gz
	ERR13765936_2.fastq.gz	Fastqsanger.gz
	ERR13765937_1.fastq.gz	Fastqsanger.gz

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jaActMedi

Project description:Actinia mediterranea

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jaActMedi1

Project description:Actinia mediterranea, genome assembly, jaActMedi1.

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ecAntMedi1

Project description:Antedon mediterranea, genomic and transcriptomic data

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Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea

Project description:The transcriptome of the planarian Schmidtea mediterranea is not well characterized. We have used RNA-Seq to characterize the transcriptome in both sexual and asexual strains of S. mediterranea from both untreated and irradiated animals. Moreover, we have performed RNA-Seq on RNA purified from FACS sorted neoblasts and differentiated cells. Together these studies expand our understanding of the planarian transcriptome and have identified strain-specific, neoblast-specific, and conserved transcripts. RNA-Seq was performed on RNA isolated from untreated and irradiated S. mediterranea animals from both the sexual and asexual strains, on FACS purified X1 neoblasts, X2 neoblasts, and Xins differentiated cells. One of the raw data files for GSM847465 is missing. The fasta file is provided at http://genome.vcell.uchc.edu/GenomeData02/Graveley_Lab_Public_Data/Planarian/S.mediterranea_SexNIRmRNA3.fa.gz

2012-04-24 | E-GEOD-34326 | biostudies-arrayexpress

Set1 and MLL1/2 target distinct sets of functionally different genomic loci in vivo: An in depth ChIP-seq analysis of H3K4me3 targets in vivo and upon Set1 and mll1 knockdown

Project description:Histone H3 lysine 4 trimethylation (H3K4me3) is known to correlate with both active and poised genomic loci, yet many questions remain regarding its functional roles in vivo. We identify functional genomic targets of two H3K4 methyltransferases, Set1 and MLL1/2, in both the stem cells (X1) and differentiated tissue (Xins) of the planarian flatworm Schmidtea mediterranea. We show that, despite their common substrate, these enzymes target distinct genomic loci in vivo, which are distinguishable by the footprint each enzyme leaves on the chromatin template, i.e., the breadth of the H3K4me3 peak. Whereas Set1 targets are broadly associated with the maintenance of the stem cell population, MLL1/2 targets are specifically enriched for genes involved in ciliogenesis. These data not only confirm that chromatin regulation is fundamental to planarian stem cell function, but also provide evidence for post-embryonic functional specificity of H3K4me3 methyltransferases in vivo. To test this, we looked at the H3K4me3 chromatin profile in WW, X1 and Xins cell types upon knockdown of set1, mll1/2, as well as WT. Examine differential binding of H3K4me3 in different experimental conditions. The experiment performed yielded a total of 58 samples.

2015-12-17 | E-GEOD-74153 | biostudies-arrayexpress

H3K36me3 is significantly more enriched at Set1-affected loci than at MLL1/2-affected loci in planarian stem cells

Project description:Histone H3 lysine 4 trimethylation (H3K4me3) is known to correlate with both active and poised genomic loci, yet many questions remain regarding its functional roles in vivo. We identify functional genomic targets of two H3K4 methyltransferases, Set1 and MLL1/2, in both the stem cells (X1) and differentiated tissue (Xins) of the planarian flatworm Schmidtea mediterranea. We show that, despite their common substrate, these enzymes target distinct genomic loci in vivo, which are distinguishable by the footprint each enzyme leaves on the chromatin template, i.e., the breadth of the H3K4me3 peak. Whereas Set1 targets are broadly associated with the maintenance of the stem cell population, MLL1/2 targets are specifically enriched for genes involved in ciliogenesis. These data not only confirm that chromatin regulation is fundamental to planarian stem cell function, but also provide evidence for post-embryonic functional specificity of H3K4me3 methyltransferases in vivo. To test this, we looked at the H3K4me3 chromatin profile in WW, X1 and Xins cell types upon knockdown of set1, mll1/2, as well as WT. Examine binding of H3K36me3 in WT in Planarian. The experiment performed yielded a total of 2 samples. These samples validate the main ChIP samples.

2015-12-17 | E-GEOD-74419 | biostudies-arrayexpress

Actinia tenebrosa

Project description:Actinia tenebrosa overview

| PRJNA415872 | ENA

Actinia equina

Project description:Actinia equina overview

| PRJNA512417 | ENA

Genome-wide analysis of planarian piRNAs

Project description:Sample dataset for the described bioinformatic pipeline (piRNAnalyzer) comprising epidermal piRNA libraries of Schmidtea mediterranea

2023-08-02 | GSE192524 | GEO

Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

2017-12-18 | PXD006238 | Pride

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