Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain.
Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Eduardo Primo-Yúfera, E-46012, Valencia, Spain.
Sci Data. 2020 Feb 27;7(1):69. doi: 10.1038/s41597-020-0412-z.
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 mip6Δ 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. Raw data, processed data and preprocessing scripts are made available.
基因表达是一个受不同分子水平调控的生物学过程，包括染色质可及性、转录以及 RNA 的成熟和运输。此外，这些调控机制与细胞代谢密切相关。在这里，我们展示了一个多组学数据集，该数据集捕获了酵母中这个多层次过程的不同方面。我们在热激时间过程中获得了野生型和 mip6Δ 菌株的 RNA-seq、代谢组学和 H4K12ac ChIP-seq 数据。Mip6 是一种 RNA 结合蛋白，它有助于环境胁迫下的 RNA 输出，并且可以说明转录后调控对控制细胞适应环境变化的贡献。该实验进行了四倍重复，并且不同的组学测量值来自相同的生物样本，这便于使用基于协方差的方法进行数据集成和分析。我们通过展示 ChIP-seq、RNA-seq 和代谢组学信号再现了核糖体基因的响应以及海藻糖代谢对热应激的贡献的现有知识来验证我们的数据集。原始数据、处理后的数据和预处理脚本均可获得。
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