RNA-Seq of human intracranially implanted U87MG-GFP cells as a function of distance from blood vessels

We devised a novel methodology for sorting stroma-free tumor cells according to their relative distance from BVs by injecting a vascular perfusion marker (Hoechst 33342). Briefly, post 3 weeks of intracranial implantation of U87MG-GFP cell line into striatum of NOD-SCID mice, the mice were injected i.v. with Hoechst dye. Mice sacrificed, tumors retrieved, single cell dissociated and FACS sorted to isolate cells that are either Hoechst Positive (Hh) or Hoechst Negative (Hl). RNA was extracted from the sorted cells and RNA-Sequencing performed.