Single cell RNA-seq of the spinal cord in a neuropathic pain model.

We produced single-cell transcriptomes from the mouse spinal cord using Drop-seq in animals modeling neuropathic pain and superficial injury (SI) controls. We used the spared nerve injury (SNI) model of neuropathic pain. ~10,000 cells from sham surgery controls and ~9,000 cells from SNI animals were sequenced. Unbiased cell clustering yielded 66 spinal cell subtypes sequenced at relatively low depth (~1200 transcripts/cell). Comparisons between SI and SNI cells were performed to investigate cell-specific differences during a neuropathic pain state. Overall design: SNI and superficial injury (SI) surgeries were conducted on the left hindleg of adult male mice. Two cohorts of mice were used (2x 5SI + 5SNI), which were batch corrected downstream. 14-days post-injury, lumbar spinal cord segments were dissociated and cells were methanol fixed. Drop-seq was performed across 4 days in groups to be batch-corrected downstream. Transcriptomes from 10 SI surgery mice and 10 SNI mice were generated. One SNI sample was removed due to dorsal root ganglion contamination (based on transcripts unique to the DRG).