1733_PancreaticIslet_BulkRNAseq
Islets from 32 mice were sequenced: 4 males and 4 females from each diet (high-fat and low-fat) and each age (20wk and 30wk), n=32. Islet RNA was extracted using the RNeasy MinElute Cleanup kit (Qiagen), RNA concentration was measured via Nanodrop and RNA quality/integrity was assessed with a BioAnalyzer (Agilent). Libraries were prepped using the SMARTer cDNA synthesis kit (Takara Bio) and sequenced at 2x150 paired end reads using a NovaSeq S4. After sequencing, reads were de-multiplexed and assigned to individual samples. FASTQ files were trimmed and filtered to remove low quality reads and aligned against a SM/J custom genome using STAR. Read counts for -cell-specific genes were normalized via TMM normalization and pairwise differential expression between cohorts was performed using edgeR31. Differential expression analysis for all 316 -cell-specific genes across select cohort comparisons reported in