E-MTAB-6882 - RNA-Seq of human U87MG-GFP cells from sub-cutan xenografts as a function of distance from blood vessels

Last updated on 19 March 2019, released on 29 April 2019
Homo sapiens
Samples (9)
Protocols (5)
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 4 weeks of sub cutaneous implantation of U87MG-GFP cell line into dorsal flank 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 located at progressive distance from blood vessels based on perfusion dye intake. Three fractions namely - Hh (close to BVs), Hm (intermediate) and Hl (farther from BVs) were FACS sorted. RNA was extracted from the sorted cells and RNA-Sequencing performed.
Experiment type
RNA-seq of coding RNA 
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-6882.idf.txt
Sample and data relationshipE-MTAB-6882.sdrf.txt
Processed data (1)E-MTAB-6882.processed.1.zip