Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)

• 1.7 million single cell transcriptomes spanning the whole adult mouse brain using 10Xv2 chemistry (WMB-10Xv2)

• 2.3 million single cell transcriptomes spanning the whole adult mouse brain using 10Xv3 chemistry (WMB-10Xv3)

• 1687 single cell transcriptomes spanning the whole adult mouse brain using the 10X Multiome chemistry (WMB-10XMulti)

• Clustering analysis of 4.0 million single cell transcriptomes spanning the whole adult mouse brain combining the 10Xv2, 10Xv3 and 10XMulti datasets (WMB-10X)

• A four level whole adult mouse brain taxonomy of cell types (WMB-taxonomy)

• 3.9 million cell spatial transcriptomics dataset spanning a single adult mouse brain with a 500 gene panel and mapped to the whole mouse brain taxonomy (MERFISH-C57BL6J-638850)

• Definition of 8 cell types neighborhoods and UMAP embeddings for fine grain visualization and analysis of neuronal types within and between brain regions (WMB-neighborhoods)

• An updated Allen CCFv3 with additional annotations for layers of Ammon’s horns, main olfactory blub and a simplified 5-level anatomical hierarchy (Allen-CCF-2020)

• CCF mapped coordinates for cells in the whole brain spatial transcriptomics dataset (MERFISH-C57BL6J-638850-CCF)

• 3.9 million cell spatial transcriptomics dataset with ~8000 genes imputed using the 500 genes in the base MERFISH-C57BL6J-638850 dataset MERFISH-C57BL6J-638850-imputed.