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bioRxiv · 10.1101/2025.03.17.643681

High-Quality Cell Capture Reveals Transcriptomic Changes After Single-Axon Injury of Mauthner Cells

Song, Z.·Zhu, L.·Shen, Y.·Yao, H.·Cai, Y.·Shi, L.·Chen, X.·Han, A.·Zhao, Z.·Qu, K.·Hu, B.
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Abstract

In vivo single-cell capture methods based on micropipettes are essential for correlating morphological characteristics with transcriptomic profiling under physiological conditions. However, they often suffer from significant contamination of off-target cells. Consequently, we developed Hip-seq, which significantly reduces heavily contaminated cells, decreases contamination levels, improves cell reproducibility, and enhances data analysis accuracy compared to patch-seq. Using Hip-seq, we found that axon regeneration failure could be due to abnormal activation of translation and the circadian clock. Axon-regenerable central neurons reactivated axon development-related genes during regeneration. And one-to-one associated analysis helped identify pro-regenerative genes.

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Song, Z., Zhu, L., Shen, Y., Yao, H., Cai, Y., Shi, L., Chen, X., Han, A., Zhao, Z., Qu, K., Hu, B.. 2025-03-18. High-Quality Cell Capture Reveals Transcriptomic Changes After Single-Axon Injury of Mauthner Cells. https://doi.org/10.1101/2025.03.17.643681

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