In order to suppress batch effects (mainly due to ambient oligodenderocyte RNA in hindbrain and spinal cord samples), we collected the unique set of genes pan-enriched in the non-neuronal clusters, as well as a set of non-neuronal genes that we believe to have tendency to appear in floating RNA (Trf, Plp1, Mog, Mobp, Mfge8, Mbp, Hbb-bs, H2-DMb2) and a set of immediate early genes (Fos, Jun, Junb, Egr1). These genes were set to zero within the neuronal clusters to avoid any batch effect when clustering the neuronal clusters. We further removed sex specific genes (Xist, Tsix, Eif2s3y, Ddx3y, Uty, and Kdm5d) and immediate early genes Egr1 and Jun from all clusters.
