Processed CODEX Data (Seurat Objects)

Seurat objects containing the raw and normalized data for:

1. 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.
2. Additional Osteo-MSC and Fibro-MSC cells that were manually annotated
3. AML/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/main

See related materials in Collection at: https://doi.org/10.25452/figshare.plus.c.7174914