Bulk RNA-sequencing of spinocerebellar tract neuron populations in cervical and thoracic sections of mouse spinal cord

We profiled populations of mouse spinocerebellar tract neurons (SCTNs) in cervical and thoracic sections of mouse spinal cord, as defined by retrograde projection labeling. For each sample, SCTNs were labeled by injecting CTB (Alexa555 conjugated form, 1µg/µl in PBS) into the cerebellum using NanojetII at P4 and examined at P6-P7. Labeled SCTNs were collected manually from 150-300µm transverse spinal cords slices were generated using a razor blade. Cells were collected from each injection experiment and then profiled using standard Illumina bulk RNA-seq protocols Overall design: We originally collected 4 biological replicates (from different mice) each of cervical and thoracic SCTN populations. For the cervical population samples, we collected 185, 182, 179, and 178 cells respectively. For thoracic population samples, we collected 310, 305, 473, and 341 cells respectively. Alignment and quantification was carried out using the STAR aligner with default parameters