Seamless integration of image and molecular analysis for spatial transcriptomics workflows
Seamless integration of image and molecular analysis for spatial transcriptomics workflows
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DOI：
10.1186/s12864-020-06832-3
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发表时间：
2020-07-14
期刊：
影响因子：
4.4
通讯作者：
Lundeberg, Joakim
中科院分区：
文献类型：
--
作者：
Bergenstrahle, Joseph;Larsson, Ludvig;Lundeberg, Joakim
背景：原位基因表达技术的最新进展构成了转录学的一个新的快速发展的领域。随着最近10倍基因组学维西姆平台的推出，这种方法开始被广泛采用。实验方案是在从较大组织样本中收集的单个组织切片上进行的。这种数据的二维性要求从样本中收集多个连续的切片，以便构建组织的全面三维地图。结果：我们已经开发了一个名为STUtility的R包，它以10x基因组Viitum数据作为输入，提供了在3D模型框架中执行标准化数据转换、多个组织切片的比对、区域注释和组合数据的可视化的功能。结论：STUtility允许用户处理、分析和可视化来自10x Genome Viitum平台的多个空间分辨RNA测序和图像数据样本。该包构建在Seurat框架之上，并使用熟悉的API和经过良好验证的分析方法。有关该软件包的介绍，请访问https://ludvigla.github.io/STUtility_web_site/.。
Background: Recent advancements in in situ gene expression technologies constitute a new and rapidly evolving field of transcriptomics. With the recent launch of the 10x Genomics Visium platform, such methods have started to become widely adopted. The experimental protocol is conducted on individual tissue sections collected from a larger tissue sample. The two-dimensional nature of this data requires multiple consecutive sections to be collected from the sample in order to construct a comprehensive three-dimensional map of the tissue. However, there is currently no software available that lets the user process the images, align stacked experiments, and finally visualize them together in 3D to create a holistic view of the tissue.Results: We have developed an R package named STUtility that takes 10x Genomics Visium data as input and provides features to perform standardized data transformations, alignment of multiple tissue sections, regional annotation, and visualizations of the combined data in a 3D model framework.Conclusions: STUtility lets the user process, analyze and visualize multiple samples of spatially resolved RNA sequencing and image data from the 10x Genomics Visium platform. The package builds on the Seurat framework and uses familiar APIs and well-proven analysis methods. An introduction to the software package is available at https://ludvigla.github.io/STUtility_web_site/.