Spatially resolved molecular and cellular atlas of the mouse brain

Han, L.; Liu, Z.; Jing, Z.; Liu, Y.; Chang, H.; Lei, J.; Peng, Y.; Wang, K.; Xu, Y.; Liu, W.; Wu, Z.; Li, Q.; Shi, X.; Zheng, M.; Wang, H.; Deng, J.; Zhong, Y.; Pan, H.; Lin, J.; Zhang, R.; Chen, Y.; Wu, J.; Xu, M.; Ren, B.; Cheng, M.; Yu, Q.; Song, X.; Lu, Y.; Tang, Y.; Yuan, N.; Sun, S.; An, Y.; Ding, W.; Sun, X.; Wei, Y.; Zhang, S.; Dou, Y.; Zhao, Y.; Zhu, Q.; Xu, J.; Wang, S.; Chen, H.; Wang, D.; Bai, Y.; Liang, Y.; Chen, M.; Xie, C.; Bo, B.; Li, M.; Zhang, X.; Ting, W.; Chen, Z.; Fang, J.; Li, S.; Jiang, Y.; Tan, X.; Zuo, G.; Xie, Y.; Li, H.; Tao, Q.; Li, Y.; Liu, J.; Li

doi:10.1101/2023.12.03.569501

bioRxiv · 10.1101/2023.12.03.569501

Spatially resolved molecular and cellular atlas of the mouse brain

Han, L.·Liu, Z.·Jing, Z.·Liu, Y.·Chang, H.·Lei, J.·Peng, Y.·Wang, K.·Xu, Y.·Liu, W.·Wu, Z.·Li, Q.·Shi, X.·Zheng, M.·Wang, H.·Deng, J.·Zhong, Y.·Pan, H.·Lin, J.·Zhang, R.·Chen, Y.·Wu, J.·Xu, M.·Ren, B.·Cheng, M.·Yu, Q.·Song, X.·Lu, Y.·Tang, Y.·Yuan, N.·Sun, S.·An, Y.·Ding, W.·Sun, X.·Wei, Y.·Zhang, S.·Dou, Y.·Zhao, Y.·Zhu, Q.·Xu, J.·Wang, S.·Chen, H.·Wang, D.·Bai, Y.·Liang, Y.·Chen, M.·Xie, C.·Bo, B.·Li, M.·Zhang, X.·Ting, W.·Chen, Z.·Fang, J.·Li, S.·Jiang, Y.·Tan, X.·Zuo, G.·Xie, Y.·Li, H.·Tao, Q.·Li, Y.·Liu, J.·Li

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Abstract

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding function of the brain. Here, using snRNA-seq and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters with single-cell resolution involving over 6 million cells as well as for 29,655 genes. We have identified new astrocyte clusters, and demonstrated that distinct cell clusters exhibit preference for cortical subregions. In addition, we identified 155 genes exhibiting regional specificity in the brainstem, and 513 long non-coding RNA exhibited regional specificity in the adult brain. Parcellation of brain regions based on spatial transcriptomic information showed large overlap with that by traditional method. Furthermore, we have uncovered 411 transcription factor regulons with spatiotemporal specificity during development. Thus, our study has discovered genes and regulon with spatiotemporal specificity, and provided a high-resolution spatial transcriptomic atlas of the mouse brain.

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Han, L., Liu, Z., Jing, Z., Liu, Y., Chang, H., Lei, J., Peng, Y., Wang, K., Xu, Y., Liu, W., Wu, Z., Li, Q., Shi, X., Zheng, M., Wang, H., Deng, J., Zhong, Y., Pan, H., Lin, J., Zhang, R., Chen, Y., Wu, J., Xu, M., Ren, B., Cheng, M., Yu, Q., Song, X., Lu, Y., Tang, Y., Yuan, N., Sun, S., An, Y., Ding, W., Sun, X., Wei, Y., Zhang, S., Dou, Y., Zhao, Y., Zhu, Q., Xu, J., Wang, S., Chen, H., Wang, D., Bai, Y., Liang, Y., Chen, M., Xie, C., Bo, B., Li, M., Zhang, X., Ting, W., Chen, Z., Fang, J., Li, S., Jiang, Y., Tan, X., Zuo, G., Xie, Y., Li, H., Tao, Q., Li, Y., Liu, J., Li. 2023-12-05. Spatially resolved molecular and cellular atlas of the mouse brain. https://doi.org/10.1101/2023.12.03.569501

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