Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, 37232, USA.
Sci Data. 2019 Jun 17;6(1):94. doi: 10.1038/s41597-019-0106-6.
Transcript levels powerfully influence cell behavior and phenotype and are carefully regulated at several steps. Recently developed single cell approaches such as RNA single molecule fluorescence in-situ hybridization (smFISH) have produced advances in our understanding of how these steps work within the cell. In comparison to single-cell sequencing, smFISH provides more accurate quantification of RNA levels. Additionally, transcript subcellular localization is directly visualized, enabling the analysis of transcription (initiation and elongation), RNA export and degradation. As part of our efforts to investigate how this type of analysis can generate improved models of gene expression, we used smFISH to quantify the kinetic expression of STL1 and CTT1 mRNAs in single Saccharomyces cerevisiae cells upon 0.2 and 0.4 M NaCl osmotic stress. In this Data Descriptor, we outline our procedure along with our data in the form of raw images and processed mRNA counts. We discuss how these data can be used to develop single cell modelling approaches, to study fundamental processes in transcription regulation and develop single cell image processing approaches.
转录本水平强烈影响细胞行为和表型，并在多个步骤中受到精细调控。最近开发的单细胞方法，如 RNA 单分子荧光原位杂交 (smFISH)，在我们理解这些步骤在细胞内的工作方式方面取得了进展。与单细胞测序相比，smFISH 可以更准确地定量 RNA 水平。此外，转录本的亚细胞定位可以直接可视化，从而能够分析转录（起始和延伸）、RNA 输出和降解。作为我们努力研究这种分析如何能够生成改进的基因表达模型的一部分，我们使用 smFISH 来定量单个酿酒酵母细胞在 0.2 和 0.4 M NaCl 渗透压胁迫下 STL1 和 CTT1 mRNA 的动力学表达。在本数据描述中，我们以原始图像和处理后的 mRNA 计数的形式概述了我们的过程和数据。我们讨论了如何使用这些数据来开发单细胞建模方法，研究转录调控的基本过程，并开发单细胞图像处理方法。
