RNA-Seq analysis of mouse dopamine neurons identifies transcriptional repression of PlexinC1 by Lmx1a and Lmx1b

In order to identify axon guidance molecules regulated by Lmx1a and Lmx1b 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 8 antero- posterior levels across the entire dopaminergic domain as revealed by TH immnostaining. Following RNA extraction, RNAseq 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.