DNA and RNA sequencing of ER+ PDXs
Paired-end libraries were constructed as in PMID: 31693904 with the following modifications. Samples were barcoded at the ligation step using Illumina unique dual barcodes adapters (cat# 20022370) and were amplified 6-8 cycles using the Library Amplification Ready-mix containing KAPA HiFi DNA Polymerase (Kapa Biosystems, Inc). For capture enrichment, libraries were pooled in equimolar ratios in groups of 10 and were hybridized in solution to the HGSC VCRome 2.1 design.  To this design, exome coverage across >3,500 clinically relevant genes that previously were covered below 20X (~2.72 Mb) was supplemented. Enriched libraries were sequenced on the NovaSeq 6000 instrument using the S4 reagent kit (300 cycles) to generate 2 x 150 bp paired-end reads. On average, 11.2 Gb of unique sequence data was generated with 95.3% of the bases in the exome design covered to 20x read depth or greater.