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Allen Brain Mouse Whole-Brain Transcriptomic Cell Type Atlas

The Mouse Whole Brain Atlas is a high-resolution transcriptomic and spatial cell-type atlas across the entire mouse brain, integrating several whole-brain single-cell RNA-sequencing (scRNA-seq) datasets. The datasets contain a total of ~4 million cells passing rigorous quality-control (QC) criteria. The integrated transcriptomic taxonomy contains 5,322 clusters that are organized in a hierarchical manner with nested groupings of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 types/clusters. The scRNA-seq data reveal transcriptome-wide gene expression and co-expression patterns for each cell type. The anatomical location of each cell type has been annotated using a comprehensive brain-wide MERFISH dataset with a total of ~4 million segmented and QC-passed cells, probed with a 500-gene panel and registered to the Allen Mouse Brain Common Coordinate Framework (CCF v3). The MERFISH data not only provide accurate spatial annotation of cell types at subclass, supertype and cluster levels, but also reveal fine-resolution spatial distinctions or gradients for cell types.

3D Developing Human Heart using MERFISH+

MERFISH+ is an spatial multi-omics platform that integrates hydrogel-based probe anchoring, automated high-throughput microfluidics, and large-format multimodal data production to enable comprehensive, subcellular resolution mapping of gene expression and chromatin organization across millions of cells within complex developing human organs.

Mouse Brain Saggital 10 Slices

MERSCOPE Imaging of WT, Trem2-R47H, 5xFAD and Trem2-R47H; 5xFAD samples

This dataset contains MERSCOPE Imaging data of 19 coronal hemispheres in WT, Trem2-R47H, 5xFAD, and Trem2-R47H; 5xFAD mice. Sections were imaged with a 300 gene panel, combined with DAPI imaging for localization of cellular nuclei.

Spatial Transcriptomic Atlas of Adult Human Basal Ganglia: H22.30.001.CX.13

This dataset is part of a whole-brain atlas effort for human and non-human primate. The data collected for this submission represent spatial transcriptomics data from core human basal ganglia regions collected using a gene panel designed to identify all known cell types identified in the snRNAseq dataset from human generated from similar regions.

VA00265 300-gene MERFISH results of human visual cortex (GW24 & GW34)

This dataset is part of a set of MERFISH experiments to identify the cell types and their locations in the developing human visual cortex. Includes samples from both GW24 and GW34 gestational stages.

MERFISH Imaging of mesocorticolimbic regions in the mouse brain

This dataset is generated by MERFISH experiments with a 300 gene panel on whole brain coronal sections covering major mesocorticolimbic areas (e.g. PFC, ventral STR, TH). After classifying transcriptomic cell types from the MERFISH expression of cell type marker genes, cell types showing differential expressions of cocaine-related genes in brain regions of interest were identified.

Subcortical Spatial Transcriptomic Atlas of the Adult Rhesus Macaque

MERSCOPE imaging of 10µm sections of core basal ganglia regions (caudate nucleus, putamen, substantia nigra, and nucleus accumbens) of fresh-frozen macaca mulatta brain slabs.