Extended Data Fig. 9: Additional nucleolar organization and sequencing analyses related to Ewing sarcoma.

a, Representative tissue sections of human Ewing sarcoma and osteosarcoma (haematoxylin and eosin staining; magnification ×400). Materials were obtained following Institutional Research Ethics Board approval (Sinai Heath Systems, 17-0103-E). The percentages of cells with one or two distinct nucleoli per nucleus are shown. Data are means ± s.d.; per cancer type, n = 5 cases (100 cells each); two-tailed t-test P = 0.0019. b, Ewing sarcoma cells (EWS502 cells) and U2OS cells with siEWSR1 display disrupted nucleoli, as indicated by the nucleolin protein, compared to their respective control IMR90 and U2OS siControl (siCTL) cells. Scale bar, 5 μm. c, Ewing sarcoma (EWS502 and TC32) cells showed increased R-loop levels across IGSs in DRIP–seq. d, Genome-wide view of sequence read alignments for DRIP–seq and RNA-seq. Chr., chromosome. e, IMR90, EWS502 and TC32 cells can exhibit similarities and differences at non-rDNA loci in sequencing read alignments from RNA-seq. f, ASOs targeting sincRNAs ameliorate nucleolar organization. Shown are representative images related to the quantifications in Fig. 4h. Images are representative of two independent experiments. Scale bar, 5 μm.