GSM7950020: Cerebellum, Het-Hit2, 430; Mus musculus; RNA-Seq
RNA forwild-type and SCA1 KI mice was extracted using TRIzol (Ambion, Life Technologies),following the manufacturers protocol and aDNA digestion was performed usingthe TURBO DNA-free Kit (Invitrogen). The Qubit RNA high sensitivity assay wasused to obtain RNA concentrations(Thermo Fisher Scientific). RNA quality waschecked via capillary electrophoresis on a 5300 fragment analyzer (AgilentBioanalyzer) using the RNA AnalysisDNF-471 RNA kit (Agilent). The NEBNext Ultra IIDirectional RNA Library Prep Kit (Illumina) with NEBNext rRNA Depletion Kit(New EnglandBiolabs) was used to prepare RNA-seq libraries, with a total of500 ng input RNA from each sample. The manufacturer'sprotocols were followed,with the following exceptions: 40× adaptor dilutions were used, and 13 cyclesof libraryamplification were performed. The resulting libraries were pooled inequimolar amounts, quantified using the NEBNextLibrary Quant Kit for Illumina(New England Biolabs), quality checked via capillary electrophoresis on the5300fragment analyzer (Agilent Bioanalzyer) using the DNF-474 HS NGS kit(Agilent). Libraries with sufficient quantitywere loaded into P2 flow cell1000/2000 by Illumina and were sequenced using paired-end, 100 base pairsequencing onthe Illumina NextSeq 2000 sequencer at the University at AlbanyRNA Institute. All datasets had total read depths greaterthan 40 million paired-end reads.