Whole exome sequencing of NT2.5 and NT2.5-LM cell lines

NT2.5-LM is a cell line derived from the parental NT2.5 cell line that provides a more proliferative and metastatic murine model of breast cancer. We used whole exome sequencing to examine mutational differences. Overall design: One microgram or more of mouse genomic DNA from each sample was analyzed by whole exome sequencing using the SureSelectXT Mouse All Exon kit (Agilent), followed by next generation sequencing using the NovaSeq 6000 S4 flow cell (Illumina) with a 2x150bp paired-end read configuration, per the manufacturer's instructions. bcl2fastq v2.15.0 (Illumina) was used to convert BCL files to FASTQ files using default parameters. Running alignments against the mm10 genome was done by bwa v0.7.7 (mem) along with Piccard-tools1.119 to add read groups and remove duplicate reads. GATK v3.6.0 base call recalibration steps were used to create a final alignment file. MuTect2 v3.6.0 was used to call somatic variants against a panel of normal using default parameters. snpEFF (v4.1) was used to annotate the variant calls and to create a clean tab separated table of variants. IGV v2.13.2 was used to identify breast cancer specific mutations from MuTect2 files. SnapGene Viewer v.6.2 was used to visually align and determine the mutations between the two cell lines against the mRNA sequences of selected genes. Annotations were created to visualize mutational differences.