RNAseq analysis of Rpl13a-snoless and wild type islets

Purpose: To gain further mechanistic insight into phenotypic differences between wild type pancreatic islets and islets with loss of function of 4 Box C/D snoRNAs from the Rpl13a locus (U32a, U33, U34 and U35a). Methods:High quality total RNA (RIN = 8.5) was prepared from hand-picked islets (n = 4 mice/genotype) using TRIZOL reagent, treated with Turbo DNAse (Thermo Fisher), and used to prepare SeqPlex RNAseq libraries (Sigma). Sequencing was performed by the Washington University Genome Technology Access Center using two lanes of Illumina HiSeq 2500, 1x50. Reads were demultiplexed and trimmed, and STAR alignment and quantification analysis was carried out using the Partek Flow platform. Uniquely aligned reads were quantified to identify genes with at least a two-fold change between genotypes with p < 0.05 and FDR step-up of 0.05. Results:We observed 2-fold or greater differences in the expression of only six genes. Conclusions: Our data indicate that loss-of-function of snoRNAs from the Rpl13a locus is associated with modest changes in mRNA abundance. Overall design: Examination of murine pancreatic islet mRNA differential expression between wild type mice and mice with loss-of-function of U32a, U33, U34, and U35a snoRNAs.

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Lee J, Harris AN, Holley CL, Mahadevan J, Pyles KD, Lavagnino Z, Scherrer DE, Fujiwara H, Sidhu R, Zhang J, Huang SC, Piston DW, Remedi MS, Urano F, Ory DS, Schaffer JE