Trastuzumab Resistance Breast Cancer Xenograft

Breast cancer cell line BT474 cells were administered subcutaneously into NCr nude mice. After randomization, mice received vehicle or trastuzumab (15mg/kg twice weekly). Tumors were categorized as control, responders, intrinsic resistance, and acquired resistance. RNA isolation was performed using RNeasy Plus kit (Qiagen) using manufacturer’s instructions. Sequencing libraries were created using Truseq stranded mRNA library preparation method from Illumina and sequenced on an Illumina NextSeq2000 sequencer. Reads were aligned to reference genome GRCh38 using HISAT2, then SAMTools was used sort and merge the alignments from multiple flow cells.