Deciphering the single-cell spatial projectomics and transcriptomics organization in PFC by SPIDER-Seq

Summary

Deciphering the connectivity, transcriptome, and spatial-omics integrated multi-module brain atlas and the underlying organization principles remains challenging. We developed a cost-effective Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) method by combining viral barcoding tracing with single-cell sequencing and spatial-omics. Leveraging SPIDER-Seq, we delineated a comprehensive integrated single-cell spatial molecular, cellular and projectomic atlas of mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct organization principle, but are coordinately configured in PFC. These projection neurons gradiently distributed in PFC aligning with their wiring patterns, and importantly, show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we depicted PFC neural transmission map, in which neural transmission molecues (neurotransmitter/neuropeptide and the receptors) distinctly express in different circuits. Finally, we predicted neuron projections by integrated gene profile and spatial information with high accuracy via machine learning. Our study could greatly facilitate to delineating brain multi-module network and understanding neural computation.

Interactively exploring our data

scRNAseq

Our scRNAseq dataset sequenced the PFC of 3 mice. It contains the transcriptome of mouse PFC and the projectome information of 24 PFC targets. Users can browse the following content through the scRNAseq page:

• scRNAseq Clustering: Select different resolutions to view cell clusters on UMAP
• Gene Expression: Select different genes to view their expression on UMAP
• Barcode Expression: Select different projections to view their expression on UMAP
• Barcode Cell Numbers: View PFC projection cell numbers in different cell clusters

Spatial data

Our spatial dataset sequenced 36 slices of mouse PFC. It contains 32 genes and 15 targets information of mouse PFC. Users can browse the following content through the spatial page:

• Spatial Clustering: Select different resolutions to view the spatial distribution of cell clusters
• Spatial Gene Expression: Select different genes to view their spatial expression
• Spatial Barcode Expression: Select different projections to view their spatial expression
• Barcode Spatial Distribution: View the spatial distribution of PFC projection neurons along anterior-posterior and ventralis-dorsalis axes

3D

3D interactive visualization of mouse PFC. Users can browse the following content through the 3D page:

• Transcriptome 3D Visualization: Select different transcriptome cell clusters to interactively view them in 3D
• Projectome 3D Visualization: Select different Projectome targets to interactively view them in 3D

Download

Download the raw and processed data from this study.