Daniel Martinez

Supplementary Figure S6 shows the increase in NF-kB activity following chemotherapy and its role in survival which is enhanced by specific TAMs and CAFs

Supplementary Table S2 links the CN number to the HTAN biospecimen numbers

Supplementary Figure S1 shows cell type markers and inferred copy number of tumors as well as characterization of malignant, Schwann cells, tumor associated macrophages and cancer associated fibroblasts at time of definitive surgery

Supplementary Figure S3 shows the WGS analysis of the diagnostic and definitive surgery including clonal evolution of ALK mutation from diagnosis to definitive surgery in one tumor.

Supplementary Table S3 provides the genes of each persister subtype signature

Supplementary Figure S5 shows the connection between NF-kB/stemness subtype and mesenchymal transcriptional state.

Supplementary Table S4 shows the most negatively enriched pathways in non-cycling persister cells by GSEA

Supplementary Figure S4 differences in persister cell composition between diagnosis and definitive surgery as well as decrease in MYC/N protein level in human samples, PDX and cell lines following chemotherapy

Supplementary Figure S2 shows the details of the pathway-based clustering algorithm including the autocorrelation pathway scores, cell cycle annotation, pathway enrichment analysis and region analysis.

Supplementary Table S1 shows the patient clinical characteristics and genetic alterations at diagnosis