title: GSM8801361: MTE-RAS PV-10 treated tumors 3; Mus musculus; RNA-Seq
library_construction_protocol: Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer's protocol. Quality control steps were performed, including TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche, Wilmington, MA). The final libraries were normalized, denatured, and sequenced on the Illumina NovaSeq 6000 sequencer with the SP-200 cycle reagent kit to generate 100-150 million 100-base read pairs per sample (Illumina, Inc., San Diego, CA). All work was performed by the Moffitt Cancer Center Molecular Genomics Core Facility (RRID:SCR_012333). Read adapters were detected using BBMerge (v37.02) (RRID:SCR_016970) and subsequently removed with cutadapt (v1.8.1) (RRID:SCR_011841). Processed raw reads were then aligned to mouse genome mm10 using STAR (v2.7.7a) (RRID:SCR_004463). Gene expression was evaluated as read count at the gene level using RSEM (v1.3.0) (RRID:SCR_000262) with the Gencode gene model vM21. Normalization and differential expression analysis between the experimental and control groups were performed using DESeq2 (RRID:SCR_015687) (27). Gene set enrichment analysis (GSEA) was performed on the ranked gene list, based on fold change between experimental and control groups, using the gseGO function from the cluster Profiler R package (v 4.6.2). The analysis focused on Gene Ontology (GO) terms.