Multi-sample snATAC-seq/snRNA-seq benchmarking datasets

Benchmarking Datasets used in: Weinand et al., Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach, In Prep. Multiome (snATAC-seq + snRNA-seq) Dataset information: Benchmarking Dataset Original Study Source Cell Phenotype Cell Count Sample Count 1 Weinand et al., Nat Commun, 2024 RA & OA inflammatory tissue Broad cell types 31,547 12 2 Weinand et al., Nat Commun, 2024 RA & OA inflammatory tissue T cell states 8,069 11 3 Weinand et al., Nat Commun, 2024 RA PBMC T cell substates 10,669 2 runs of 4 pooled samples each 4 Cheong et al., Cell, 2023 COVID-19 & healthy PBMC Broad cell types 197,360 30 5 Cheong et al., Cell, 2023 COVID-19 & healthy PBMC HSPC states 27,979 28 Data provided per Dataset: inputs: All inputs for our command-line tool: https://github.com/immunogenomics/snATAC_benchmark/ outputs: Selected outputs from our tool, namely embeddings, NN metrics, LISI metrics, and UMAP coordinates for all dataset, feature, method, and correction combinations UMAPs: UMAP plots for use in our website: https://immunogenomics.io/snATAC_benchmark/ Note: dataset4 inputs were too big to upload in one zip file, so they were uploaded in four zip files.本基准测试数据集应用于以下研究： Weinand 等人，《通过多模态引导策略整合多样本单细胞核ATAC测序（single-nucleus ATAC-seq，snATAC-seq）数据集的有效方案定义》，待发表（In Prep） 多组学（snATAC-seq + 单细胞核RNA测序（single-nucleus RNA-seq，snRNA-seq））数据集详情如下： ### 基准测试数据集详情表 | 序号 | 原始研究 | 样本来源 | 细胞表型 | 细胞计数 | 样本计数 | | :---: | :--- | :--- | :--- | :---: | :---: | | 1 | Weinand et al., *Nat Commun*, 2024 | 类风湿关节炎（RA）与骨关节炎（OA）炎症组织 | 宽泛细胞类型 | 31,547 | 12 | | 2 | Weinand et al., *Nat Commun*, 2024 | 类风湿关节炎（RA）与骨关节炎（OA）炎症组织 | T细胞状态 | 8,069 | 11 | | 3 | Weinand et al., *Nat Commun*, 2024 | 类风湿关节炎（RA）外周血单个核细胞（peripheral blood mononuclear cell，PBMC） | T细胞亚状态 | 10,669 | 每组包含4个混合样本，共2组 | | 4 | Cheong et al., *Cell*, 2023 | COVID-19患者与健康人外周血单个核细胞（PBMC） | 宽泛细胞类型 | 197,360 | 30 | | 5 | Cheong et al., *Cell*, 2023 | COVID-19患者与健康人外周血单个核细胞（PBMC） | 造血干细胞与祖细胞（hematopoietic stem and progenitor cell，HSPC）状态 | 27,979 | 28 | 各数据集配套提供的数据如下： 1. **输入数据**：本研究命令行工具的全部输入文件，工具开源仓库地址：https://github.com/immunogenomics/snATAC_benchmark/ 2. **输出数据**：本工具生成的精选分析结果，涵盖所有数据集、特征、分析方法与校正组合对应的嵌入向量、最近邻（Nearest Neighbor，NN）指标、局部逆桑普森指数（Local Inverse Simpson’s Index，LISI）指标及UMAP坐标 3. **UMAP可视化图表**：用于本研究官方网站的UMAP绘图，官网地址：https://immunogenomics.io/snATAC_benchmark/ 备注：数据集4的输入文件体积过大，无法打包为单个压缩包，因此拆分为4个压缩包上传。