Next Generation Sequencing Facilitates Quantitative Analysis of control and HPK1-M46 Transgenic Mice Transcriptomes

Purpose: The goals of this study are to compare cerulean treated acinar cells of HPK1-M46 transgenic mice transcriptome profiling (RNA-seq) to study HPK1 pathway Methods: Total RNA was prepared from mouse pancreata harvested 24 hours after Cerulean treatment using RNeasy Mini/Micro Kit according to the manufacturer's instructions. RNA quality was measured by the Agilent TapeStation 2200 (Agilent, Santa Clara, CA). RNA samples with RNA integrity numbers of =7 were processed for RNA-seq transcriptome analysis. Results: The RNA-seq libraries were pooled and sequenced, 83 bp single read, on Illumina NextSeq 550 or Illumina NovaSeq 6000 (Illumina, San Diego, CA). All sequencing data were demultiplexed and converted into fastq files by Illumina bcl2fastq2 v2.17.14. Filtered sequence reads were mapped to reference genome mm10 using STAR aligner with default settings. Conclusions: Our study represents the first detailed analysis of HPK1 transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Overall design: Total RNA profiles of Cerulean treated wild type (B) and HPK1/B (HC), M46/B (MC) mice pancreas were generated; Total RNA profiles of KC and KMC mice pancreas were generated