RNA-seq of ER+ BC xenografts under estrogen withdrawal
Cell lines indicated were grown in DMEM supplemented with 10% FBS.  Cells were injected orthotopically into JNu mice.  Mice were also given subcutaneous (s.c) 17-?-estradiol pellets as well.  Tumors were monitored until they reached volumes of approximately 400mm3.  Estrogen withdrawal treatments were performed by removing the supplemented s.c Estradiol pellet for either 0, 6, or 90 days.  At indicated time points tumors were harvested, fixed in 10% formalin, and embedded in paraffin blocks.  RNA extractions were done using Qiagens RNeasy FFPE kit and performed according to manufacturer protocols. Illumina RNA-Access kit for FFPE was used with 40ng of RNA as input for the construction of sequencing libraries. All libraries were pooled onto a single NextSeq500 instrument and sequenced as 75bp paired-end reads.