Transplantation of neural stem or progenitor cells (NSPCs) shows promise for treating neurological conditions, but it is unclear how such cells respond to transplantation. By using various techniques, including RNA sequencing, the authors found that a number of the cellular properties of NSPCs changed after they were implanted into spinal cord injuries in mice. Of note, various genes showed environment-dependent changes in expression or splicing, and overall transcription was suppressed. The effects of the graft environment on NSPCs should be considered in future clinical applications.