RNA sequencing of necrotic core and non-necrotic rim of tumors from 4T1 cell xenografts into rat

The goal of this experiment was to determine differences in RNA expression between the central necrotic tumor core and the non-necrotic rim region in orthotopic xenograft models of 4T1 cells transplanted into immunocompromised rat hosts. These samples are derived from tissues obtained from 4T1 spheroids transplanted orthotopically into the mammary fat pads of SRG OncoRats. 4T1 cells were cultured as spheroids in suspension for 24-hours prior to transplantation in 2% matrigel. 600,000 cells in a 1:1 mixture of matrigel and DMEM/F12 were transplanted orthotopically into the right T4 fat pads of SRG rats. At day 27 post transplanation, primary tumors and lungs were collected. The primary tumors were cut in half to expose the cross-section, and the tumors were dissected to isolate the necrotic core region and the non-necrotic rim region. Samples were snap frozen and sent to Genewiz-Azenta for RNA extraction, library prep, and next-gen sequencing. 4T1 cells were orthotopically transplanted into mammary fat pads of SRG hosts. Tumor and lungs were collected. Tumors were dissected into necrotic and non-necrotic region, and submitted separately for sequencing RNA sequencing. Rat mammary glands (no transplant) and 4T1 cell pellets were sequences as mono-species rat and mouse controls to evaluate the species disambiguation algorithm.