美国哈佛医学院Chris Sander等研究人员合作开发了scPerturb，统一的单细胞扰动数据。相关论文于2024年1月26日在线发表在《自然—方法学》杂志上。

为了促进计算方法的开发和基准测试，研究人员收集了一组44个公开可用的单细胞扰动-反应数据集，其中包括转录组学、蛋白质组学和表观基因组学等分子读数。研究人员采用统一的质量控制管线并统一特征注释。由此产生的信息资源scPerturb可以帮助开发和测试计算方法，并促进数据集之间的比较和整合。

研究人员介绍了用于量化扰动效应和显著性检验的能量统计（E-statistics），并展示了作为单细胞表达谱集之间一般距离测量的E-distance。研究人员说明了E-statistics在量化扰动的相似性和有效性方面的应用。扰动-响应数据集和E-statistics计算软件可在scperturb.org上公开获取。这项工作为使用单细胞扰动数据的研究人员提供了信息资源，并为实验设计（包括最佳细胞数和读取深度）提供了建议。

据介绍，数据互操作性差阻碍了对越来越多的单细胞扰动数据集进行分析。

附：英文原文

Title: scPerturb: harmonized single-cell perturbation data

Author: Peidli, Stefan, Green, Tessa D., Shen, Ciyue, Gross, Torsten, Min, Joseph, Garda, Samuele, Yuan, Bo, Schumacher, Linus J., Taylor-King, Jake P., Marks, Debora S., Luna, Augustin, Blthgen, Nils, Sander, Chris

Issue&Volume: 2024-01-26

Abstract: Analysis across a growing number of single-cell perturbation datasets is hampered by poor data interoperability. To facilitate development and benchmarking of computational methods, we collect a set of 44 publicly available single-cell perturbation–response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We apply uniform quality control pipelines and harmonize feature annotations. The resulting information resource, scPerturb, enables development and testing of computational methods, and facilitates comparison and integration across datasets. We describe energy statistics (E-statistics) for quantification of perturbation effects and significance testing, and demonstrate E-distance as a general distance measure between sets of single-cell expression profiles. We illustrate the application of E-statistics for quantifying similarity and efficacy of perturbations. The perturbation–response datasets and E-statistics computation software are publicly available at scperturb.org. This work provides an information resource for researchers working with single-cell perturbation data and recommendations for experimental design, including optimal cell counts and read depth.

DOI: 10.1038/s41592-023-02144-y

Source: https://www.nature.com/articles/s41592-023-02144-y