Ontology highlight
ABSTRACT:
PROVIDER: PRJNA668394 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:RNA-seq of diurnal gene expression of Cyanophora paradoxa, Porphyridium purpureum, Klebsormidium nitens, Physcomitrella patens, Selaginella moellendorfii and Picea abies
| PRJEB29012 | ENA
Project description:Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of genomes and transcriptomes. The use of this technology for transcriptome analysis has many advantages over hybridization based technologies, including higher sensitivity and specificity, and eliminates the need for probe design. Using Illumina sequencing of mRNAs, we have captured the global transcriptional profiles of the developmental cycles of D. discoideum and D. purpureum. The morphology and transcriptional profiles in these two species have been largely conserved even after greater than 300 million years of divergence. We also captured the transcriptional profiles of prespore and prestalk cells from both species. The RNA-seq results correlate well with previously known markers and reveal many new transcripts with unique developmental regulation and cell type enrichment. Our analysis provides the first complete picture of the transcriptional landscape in both D. discoideum and D. purpureum. Transcriptional abundance of over 13,900 genome elements from seven time points of development, and prespore/prestalk cell types will be available through a graphical, highly-interactive, explorative web interface at: http://www.ailab.si/dictyexpress , which currently displays all of our published microarray data. Sequence coverage at a single nucleotide resolution will also be available through an interactive genome browser. These data, from morphology to genome to transcriptome, provide a global picture of the developmental cycles of D. discoideum and D. purpureum and will facilitate the functional classification of genes, as well as discovery of novel genes, splice variants, regulatory elements and non-coding RNAs. Keywords: Transcriptome Analysis Examination of 7 developmental time points in two cell types with 2 biological replicates for each sample.
2010-03-12 | E-GEOD-17637 | biostudies-arrayexpress
Project description:Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of genomes and transcriptomes. The use of this technology for transcriptome analysis has many advantages over hybridization based technologies, including higher sensitivity and specificity, and eliminates the need for probe design. Using Illumina sequencing of mRNAs, we have captured the global transcriptional profiles of the developmental cycles of D. discoideum and D. purpureum. The morphology and transcriptional profiles in these two species have been largely conserved even after greater than 300 million years of divergence. We also captured the transcriptional profiles of prespore and prestalk cells from both species. The RNA-seq results correlate well with previously known markers and reveal many new transcripts with unique developmental regulation and cell type enrichment. Our analysis provides the first complete picture of the transcriptional landscape in both D. discoideum and D. purpureum. Transcriptional abundance of over 13,900 genome elements from seven time points of development, and prespore/prestalk cell types will be available through a graphical, highly-interactive, explorative web interface at: http://www.ailab.si/dictyexpress , which currently displays all of our published microarray data. Sequence coverage at a single nucleotide resolution will also be available through an interactive genome browser. These data, from morphology to genome to transcriptome, provide a global picture of the developmental cycles of D. discoideum and D. purpureum and will facilitate the functional classification of genes, as well as discovery of novel genes, splice variants, regulatory elements and non-coding RNAs. Keywords: Transcriptome Analysis
2010-03-12 | GSE17637 | GEO
Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>
2020-02-14 | MTBLS1320 | MetaboLights