Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization.
Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization.
复制标题
DOI：
10.1016/j.xpro.2023.102047
复制
发表时间：
2023-03-17
期刊：
影响因子：
--
通讯作者：
Ting, Angela H.
中科院分区：
文献类型：
--
作者：
Sona, Surbhi;Bradley, Matthew;Ting, Angela H.
有大量的软件利用单细胞RNA-seq（scRNA-seq）数据来解卷积空间转录组学斑点，这些斑点目前还没有达到单细胞分辨率。在这里，我们提供了用于实现Seurat和Giotto包的协议，以阐明我们示例人类输尿管scRNA-seq数据集中的细胞类型分布。我们还描述了如何使用Seurat库创建一个独立的交互式Web应用程序来可视化和共享我们的结果。有关本方案使用和执行的完整详细信息，请参见Fink等人。（2022年）。将scRNA-seq图谱与空间表达数据整合的两种方法比较这些方案以确定哪种方案最适合给定数据集的指南下载样本数据并设置两种方案运行用于整合空间数据的交互式RShiny应用程序的代码出版商说明：进行任何实验方案都需要遵守当地机构的实验室安全和伦理指南。有大量的软件利用单细胞RNA-seq（scRNA-seq）数据来解卷积空间转录组学斑点，这些斑点目前还没有达到单细胞分辨率。在这里，我们提供了用于实施Seurat和Giotto包的方案，以阐明我们的示例人类输尿管scRNA-seq数据集中的细胞类型分布。我们还描述了如何使用Seurat库创建一个独立的交互式Web应用程序来可视化和共享我们的结果。
There is a wealth of software that utilizes single-cell RNA-seq (scRNA-seq) data to deconvolve spatial transcriptomic spots, which currently are not yet at single-cell resolution. Here we provide protocols for implementing Seurat and Giotto packages to elucidate cell-type distribution in our example human ureter scRNA-seq dataset. We also describe how to create a stand-alone interactive web application using Seurat libraries to visualize and share our results. For complete details on the use and execution of this protocol, please refer to Fink et al. (2022). Two approaches for integrating scRNA-seq profiles with spatial expression data Guide for comparing these protocols to determine which is best for a given dataset Scripts for download of sample data and setup for both protocols The code to run an interactive RShiny app for integrated spatial data Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. There is a wealth of software that utilizes single-cell RNA-seq (scRNA-seq) data to deconvolve spatial transcriptomic spots, which currently are not yet at single-cell resolution. Here we provide protocols for implementing Seurat and Giotto packages to elucidate cell-type distribution in our example human ureter scRNA-seq dataset. We also describe how to create a stand-alone interactive web application using Seurat libraries to visualize and share our results.
影响因子：
12.3
作者：
Dries R;Zhu Q;Dong R;Eng CL;Li H;Liu K;Fu Y;Zhao T;Sarkar A;Bao F;George RE;Pierson N;Cai L;Yuan GC
通讯作者：
Yuan GC
影响因子：
64.5
作者：
Hao Y;Hao S;Andersen-Nissen E;Mauck WM 3rd;Zheng S;Butler A;Lee MJ;Wilk AJ;Darby C;Zager M;Hoffman P;Stoeckius M;Papalexi E;Mimitou EP;Jain J;Srivastava A;Stuart T;Fleming LM;Yeung B;Rogers AJ;McElrath JM;Blish CA;Gottardo R;Smibert P;Satija R
通讯作者：
Satija R
影响因子：
11.8
作者：
Fink, Emily E.;Sona, Surbhi;Tran, Uyen;Desprez, Pierre-Emmanuel;Bradley, Matthew;Qiu, Hong;Eltemamy, Mohamed;Wee, Alvin;Wolkov, Madison;Nicolas, Marlo;Min, Booki;Haber, Georges-Pascal;Wessely, Oliver;Lee, Byron H.;Ting, Angela H.
通讯作者：
Ting, Angela H.