Processed CODEX Data (Seurat Objects)

Seurat objects containing the raw and normalized data for:Normal bone marrow (NBM) atlas: contains all cells obtained through segmentation after filtering and QC. Includes coarse and fine level of annotations that were obtained through an iterative process of subclustering. Neighborhood analysis results are included as a metadata column. Additional Osteo-MSC and Fibro-MSC cells that were manually annotatedAML/NSM CODEX data: contains all cells after filtering for 3 diagnostic and 2 post-therapy AML samples as well as 3 negative staging marrow samples. Cell labels were derived through reciprocal principal component analysis (RPCA) reference mapping onto the normal bone marrow atlas. Neighborhood analysis was conducted separately for AML Diagnostic, AML Post-Therapy, and NSM samples. Neighborhoods were manually annotated for each set. The results of the neighborhood analysis were merged and included in the metadata of the Seurat object. All normalized data is stored in the Seurat assay object. Markers that were not included in normalization and downstream analysis are included with raw values as a metadata column. Full source code used to generate these objects can be found on GitHub: https://github.com/shovikb94/spatial-bonemarrow-atlas/tree/mainSee related materials in Collection at: https://doi.org/10.25452/figshare.plus.c.7174914

本数据集包含两类Seurat对象（Seurat），分别存储原始与标准化测序数据：
正常骨髓（Normal Bone Marrow, NBM）图谱：涵盖经过滤与质量控制（QC）后通过细胞分割得到的全部细胞，包含通过亚聚类迭代流程获得的粗粒度与细粒度细胞注释；邻域分析结果以元数据列形式收录；此外补充了经手动注释的骨-间充质干细胞（Osteo-MSC）与纤维母-间充质干细胞（Fibro-MSC）细胞群。
AML/NSM CODEX数据：包含针对3份诊断性急性髓系白血病（AML）样本、2份治疗后AML样本以及3份阴性分期骨髓样本完成过滤后的全部细胞；细胞标签通过反向主成分分析（reciprocal principal component analysis, RPCA）将数据映射至上述正常骨髓图谱得到；分别针对AML诊断样本、AML治疗后样本与NSM样本开展独立邻域分析，并对各组邻域进行手动注释；将邻域分析结果合并后以元数据列形式加入Seurat对象。所有标准化数据存储于Seurat实验（assay）对象中；未纳入标准化与下游分析的标记基因以原始值形式作为元数据列收录。
用于生成上述Seurat对象的完整源代码可在GitHub平台获取：https://github.com/shovikb94/spatial-bonemarrow-atlas/tree/main。相关数据集材料可于Figshare集合中获取：https://doi.org/10.25452/figshare.plus.c.7174914

搜集汇总

背景与挑战

背景概述

该数据集包含处理后的CODEX数据，主要涉及正常骨髓和AML/NSM样本的细胞分析，包括细胞注释、邻域分析和标准化数据，适用于空间蛋白质组学和癌症细胞生物学研究。