NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors. Bonine et al.

Neuroblastoma, a rare embryonic tumor arising from neural crest development, is responsible for 15% of pediatric cancer-related deaths. Recently, several single-cell transcriptome studies were performed on neuroblastoma patient samples to investigate the cell-of-origin and tumor heterogeneity. However, these individual studies involved a small number of tumors and cells, limiting the conclusions that could be drawn. To overcome this limitation, we integrated seven single-cell or single-nucleus data sets into a harmonized cell atlas covering 362,991 cells across 68 patient samples. We use this atlas to decipher the transcriptional landscape of neuroblastoma at single-cell resolution revealing associations between transcriptomic profiles and clinical outcomes within the tumor compartment. In addition, we characterize the complex immune cell landscape and uncover considerable heterogeneity among tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with new data and using it as a reference for data-driven cell-type annotation.

seuratObj_NBAtlas_share_v20240130.rds: Seurat Object of the NBAtlas. Be aware, using this object requires roughly 14 GB of memory.
SeuratObj_Share_50kSubset_NBAtlas_v20240130.rds: Light-weight version of the NBAtlas (50 k subset) for portable use.
# v2:
seuratObj_NBAtlas_share_v20241203.rds: Cleaned Seurat Object of the NBAtlas (doublets from the zooms filtered out).
# v3:
SeuratMeta_TumorZoom_NBAtlas_v20250228.rds: Metadata of tumor zoom, for annotation use "clusters" or "cluster_nr", for umap coordinates use "scviUMAP_1" and "scviUMAP_2". This metadata can be used to subset the entire atlas Seurat object to obtain a tumor zoom Seurat object.