Illumina NovaSeq 6000 paired end sequencing; Bl6 Ndp-KO systemic gene therapy whole cochlea samples
Mice were sacrificed by cervical dislocation. The inner ear was immediately isolated from surrounding tissue and the cochlea was separated from the vestibular region, the stapedial artery removed and the cochlea snap frozen Total RNA was extracted  using  a  modification  of  a  published  protocol  (PMID 25818515)  (TRI  Reagent®  93289-25ML Sigma-Aldrich,  DirectZol  kit).  RNA  was  eluted  in  40-50  μl  of  nuclease-free  water  and analysed  using  the  by  NanoDropTM  2000  (Thermo  Scientific)  and  Agilent  Bioanalyzer platforms. LIbraries were constructed for Illumina, strand-specific RNA-seq with PolyA selection according to standard protocols by Azenta Lifesciences