Transcriptome Profiling of Lmx1a/b cKO Mice

RNA sequencing was performed on three biological replicates for the control and four biological replicates for Lmx1a/b cKO mice. For each sample, two technical replicates were performed. For each E15.5 embryo used, VTA and SNpc were dissected from eight antero–posterior levels across the entire DA domain as revealed by TH immnostaining. Following RNA extraction, RNA-seq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown and sequenced on Illumina HiSeq2500 by 150-bp paired-end sequencing. One sample was excluded before the sequencing because the amount of RNA was too low to measure the RNA quality. Reads were aligned using STAR aligner (version 2.4.2a) to the mouse genome assembly GRCm38. Raw read counts per gene were obtained using featureCount in the R package Rsubread with the GENCODE annotation vM8. The gene differential expression analysis was done using DeSeq2^{50 (link)}. We only considered genes with >10 reads across all of the samples. A total of 225 genes with adjusted p value <0.2 were reported as being significantly differentially expressed. Data are available at Array Express under accession number E-MTAB-5986.