Figure 5: FACS and genomic analysis of VE-cadherin-positive CDX tumour cells.

(a) Schematic representing generation of CDX3 and subsequent processing of samples for FACS of human (Mouse MHC1^−VE) subpopulations based on VE-cadherin^+VE and VE-cadherin^−VE expression. (b) Flow Cytometry dot plots showing gating strategies used for cell sorting. Left panels, forward light scatter versus anti-mouse anti-MHC1 staining. Right panels, side light scatter versus anti-human, anti-VE-cadherin staining. Gating strategies set according to relevant controls (see the ‘Methods’ section). (c) CNA profiles from mice bearing CDX3 tumours (CDX3(a) and CDX3(b)) FACS-sorted mouse MHC^−VE, bulk tumour/VE-cadherin^+VE/VE-cadherin^−VE and patient 3 germline control (white blood cells). The GC-normalized and mappability corrected read counts (log₂ scale) were segmented using Hidden Markov Model (HMM), red=copy-number gains, blue=copy-number losses. (d) VAF of TP53 (p.Y220C) mutation in sorted cell subpopulations. (e) Read alignment plots from representative samples demonstrate the presence of variant TP53 allele (p.Y220C) in bulk tumour, VE-cadherin^+VE and VE-cadherin^−VE fractions, but absent in germline patient control.