Genechip mouse genome 430 2.0 arrays

12 μm-thick cryosections were collected from E16.5 C57/Bl6 mouse hindbrains fresh frozen in OCT and mounted on RNase-free, PEN-foil covered glass slides (Zeiss), followed by dehydration and staining with 1% Cresyl Violet prior to LCM using PALM Micro-beam system (Zeiss). Every 5^th section was collected on a glass reference slide and stained with guinea pig anti-ISL1/2 primary (gift from Tom Jessell, Columbia University) and horse radish peroxidase (HRP)-conjugated anti-guinea pig secondary (Sigma-Aldrich) antibodies. Antibody binding was visualized with a 3,3′-Diaminobenzidine tetrahydrochloride (DAB) chromogenic HRP stain (Sigma-Aldrich) to confirm the range of sections containing FMNs. M, I, DL and L subnuclei from sets of 3 hindbrains were collected directly into lysis buffer, pooled, processed for RNA extraction (Absolutely RNA, NanoPrep kit, Stratagene, La Jolla, CA). RNA integrity number (RIN) was assessed on the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). Approximately 1.5ng of purified RNA was amplified in the WT-Ovation Pico RNA Amplification System (Nugen) and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays (Kaplan et al., 2014 (link)).