Data and code from: Transcriptional code for circuit integration in the injured brain by transplanted human neurons
Data files
Sep 30, 2026 version files 90.06 MB
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ctip2kd_transplant.rds
26.36 MB
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machine_learning_model_for_upload.ipynb
18.23 KB
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README.md
1.35 KB
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transplant_brain.rds
56.91 MB
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transplant_spinalcord.rds
6.78 MB
Abstract
Neural transplantation holds the potential to repair damaged neural circuits in neurological diseases. However, it remains unknown how the grafted neurons project axons to and make functional connections with the appropriate targets to repair the damaged circuit at the adult stage. Here, we report that human cortical progenitors, transplanted into the ischemic mouse motor cortex, matured and integrated into cortical and subcortical neural circuits, including the corticospinal tract. Neuronal tracing combined with single-nuclei RNA sequencing revealed the close relationship between the transcription profiles of a cortical neuronal subtype, especially those of axon guidance and synapse assembly, with the specific target projection and synapse organization. Machine learning-based regression further identified the transcriptional codes for the targeted projection and circuit integration to reconstruct the damaged circuits. Our finding opens a promising strategy for treating neurological diseases through promoting regeneration and neural transplantation.
Dataset DOI: 10.5061/dryad.4j0zpc8qd
Description of the data and file structure
snRNA-seq data and new codes
Files and variables
File: transplant_spinalcord.rds
Description: snRNA-seq data from retrograde AAV injection of GFP/RFP in the spinal cord (Figure 4E and 4F).
Transplanted cortical neuronal subtypes project to specific brain regions revealed by MRT-seq.
File: ctip2kd_transplant.rds
Description: the snRNA-seq data for barcoded AAV injection in Figure 5 and S8.
Grafted human cortical neurons alter the projection pattern when CTIP2 is knocked down.
File: transplant_brain.rds
Description: snRNA-seq data for barcoded AAV injection in Figure 4, 6, S1, S7, and S9.
Transplanted cortical neuronal subtypes project to specific brain regions revealed by MRT-seq.
Transcriptional codes for grafted cortical neurons.
File: machine_learning_model_for_upload.ipynb
Description: machine learning model for transcriptional codes of neuronal subtypes.
Transcriptional codes for grafted cortical neurons.
Code/software
Software: RStudio (with R3.6.0+)
Packages: Seurat (v4.0 or above)
Software: Jupyter Notebook (with Python 3.8)