Luecken multiome human bone marrow 2021 s4d8 cellular structure

Dataset published by Luecken et al. 2021 which contains data from human bone marrow measured through joint profiling of single-nucleus RNA and chromatin accessibility using the 10X Genomics Single Cell Multiome ATAC + Gene Expression Kit. All files stored in this entry are from sample 4 donor 8 and contain updated/additional objects depending on the preprocessing step applied. <br> The respective raw files can be downloaded here:<br> <strong>File description</strong> <em>s4d8_clustered.h5ad</em>: Clustered and normalized cells by features matrix. This file only includes cells from the sample of site 4, donor 8. Cells that did not pass QC are removed. AnnData object includes raw counts (under .X) and normalized counts (under <em>adata.layers['scran_normalization']</em>). <em>reference_embedding.h5ad</em>: 10-dimensional integrated embedding of the dataset as described above (excluding site 4, donor 8 sample) created by integrating with scVI, using site + donor as the batch variable. <em>gene_info.csv</em>: table listing the genes (in order) used for the scVI integration model, and needed for query-to-reference mapping with scArches <em>model.pt</em>: integration scVI model of the bone marrow reference, needed for query-to-reference mapping with scArches <br> <strong>Citation</strong> Luecken, M. D. <em>et al.</em> A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. Thirty-fifth Conference on Neural Information Processing Systems Datasets and Benchmarks Track (2021). <br> <strong>Original data link</strong> https://openproblems.bio/neurips_docs/data/dataset/本数据集由Luecken等人于2021年发布，包含通过10X Genomics单细胞多组学ATAC+基因表达试剂盒（10X Genomics Single Cell Multiome ATAC + Gene Expression Kit）对人类骨髓开展单细胞核RNA与染色质可及性联合谱分析得到的数据。本条目下的所有文件均来自供体8的样本4，根据所采用的预处理步骤不同，包含更新或新增的分析对象。 相应的原始文件可在此处下载： **文件说明** *s4d8_clustered.h5ad*：按特征完成聚类与归一化的细胞矩阵文件。该文件仅包含供体8、位点4样本的细胞，已移除未通过质量控制（Quality Control, QC）的细胞。该AnnData对象包含原始计数（存储于.X中）与归一化计数（存储于adata.layers['scran_normalization']中）。 *reference_embedding.h5ad*：本数据集的10维整合嵌入文件（不含供体8、位点4样本），通过以位点+供体作为批次变量，利用scVI整合构建得到。 *gene_info.csv*：按排序列出用于scVI整合模型的基因的表格，同时是使用scArches进行查询-参考映射所需的配套文件。 *model.pt*：骨髓参考数据集的scVI整合模型文件，是使用scArches开展查询-参考映射的必备文件。 **引用文献** Luecken, M. D. 等人. 单细胞中DNA、RNA与蛋白质的预测及整合沙箱. 第三十五届神经信息处理系统会议数据集与基准追踪 (2021). **原始数据链接** https://openproblems.bio/neurips_docs/data/dataset/