Project description:Bulk RNA-Seq datasets were generated for the roots and leaves of Pistia stratiotes in order to compare expression of nutrient transporters between the tissues
Project description:We performed RNA-seq on microdissected regions of Lemna minor (clone 8623) and Spirodela polyrhiza (clone 9509) fronds, alongside the related aroids Pistia stratiotes (water lettuce) and Colocasia esculenta (taro), to define region-specific transcriptomes and compare organ-identity programmes across species. Transcript abundance was quantified with Salmon v1.10.0 and cross-species comparisons were performed on 6,230 one-to-one orthologues identified by OrthoFinder v3.0.1b1.
Project description:This model was reconstructed from single-nucleus RNA-seq (snRNA-seq) data of human postmortem brain and curated using published metabolomics data from human iPSC-derived neurons and cerebrospinal fluid (CSF), together with gene expression data from the Human Protein Atlas. It more accurately simulates human neuronal metabolic flux in neurodegenerative conditions such as Alzheimer's disease (AD).
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>