title: GSM8974397: Liver tumor, 4 weeks post AAV8-YFP injection, mouse 1; Mus musculus; RNA-Seq
library_construction_protocol: After 4 (early time point) or 8 (late time point) weeks following AAV injection mice were anesthetized using ketamine/xylazine and liver tumor tissues were collected, flash frozen in liquid nitrogen, and stored for molecular analysis. For RNA-sequencing, frozen tumor tissue (~30 mg) was homogenized with Buffer RLT (RNeasy Mini Kit, Qiagen # 74106), and RNA isolation was performed using RNeasy kit (Qiagen, ID: 74106) following the manufacturer's instructions. Sample quality was assessed using the Agilent 2100 Bioanalyzer G2938C with the Aligent RNA 6000 Nano Kit (Agilent; Santa Clara, CA, USA). Only samples passing the RNA integrity number threshold of 7.0 were used for sequencing. mRNA was enriched using NEBNext Poly(A) mRNA Isolation Module (NEB, Ipswich, MA, USA) followed by library preparation using NEBNext® Ultra™ II Directional RNA library kit (NEB, Ipswich, MA, USA). Next-generation sequencing was conducted at the McMaster Genomics Facility, Farncombe Institute, McMaster University, using Illumina HiSeq 1500 (Illumina; San Diego, CA, USA). Samples were randomly distributed across lanes of a HiSeq Rapid v2 flow cell to eliminate lane-specific effects and single-end 50 bp reads were generated at 12.5 million clusters per sample.