Bulk RNA-sequencing of cell populations in mouse Anterior Lateral Motor (ALM) cortex based on four projection targets

We profiled populations of mouse neurons in the Anterior Lateral Motor (ALM) cortex, as defined by retrograde projection labeling. For each sample, we injected one of four regions (thalamus, IRN in medulla, superior colliculus, or pons) using the retrograde virus rAAV2-retro with a fluorescent repoter, and collected cells in the ALM whose projections to the target area were labelled. 50-120 cells were collected from each injection experiment and then profiled using standard bulk RNA-seq protocols We originally collected 7 biological replicates (from different mice) each of thalamus-projecting and medulla-projecting cells, and 3 biological replicates each of super colliculus-projecting and pons-projecting cells. After alignment and quantification of the RNA-seq data, principal component analysis identified one thalamus-projecting and one medulla-projecting sample as outlier samples, and these have been labeled as such in the sample titles