A method to investigate muscle target-specific transcriptional signatures of single motor neurons

To investigate target-specific transcriptional signatures of single motor neurons, here we combine ex-ovo retrograde axonal labelling in mid-gestation chicken embryos with manual isolation of individual fluorescent cells and Smart-seq2 single-cell RNA-sequencing. We validate our method by injecting the EMR and FDQ wing muscles and harvest a total of 50 fluorescently labeled cells, in which we detect upto 10000 transcribed genes. Additionally, we present visual cues and cDNA metrics predictive of sequencing success. SMART-seq2 single neuron RNA-seq of manually picked motor neurons identified by axonal backfill from EMR and FDQ muscles of Day 9 chicken embryos.