Extended Data Fig. 1: Full and additional whole population PDTO sequencing datasets of PDTO-9.

a, Full PDTO-9 dataset of experiment shown in Fig. 1b. Karyotype heatmap showing 62 cells derived from a clonal PDTO-9 structure expressing transgenic H2B-Dendra2 and consisting of 67 cells (93% recovery). Reciprocal gains and losses are indicated with red boxes. Dashed boxes indicate CNA events where a reciprocal loss or gain is missing. Sub-chromosomal CNAs were counted as events when represented in more than one cell. Scalebar is 10μm. b, As in a. 64 out of 72 cells provided quality sequence (89% recovery). Parallel emergence of de novo whole-chromosome missegregations of Chr.15 (I, II) was determined by co-occurrence of a sub-chromosomal CNA in Chr.3. c, As in a. 33 out of 37 cells provided quality sequence (89% recovery). Two lineages show amplified sub-chromosomal CNAs in one cell, while all other cells in the lineage show a reciprocal loss of the same region (III. IV). Consistent with replication and collective missegregation of acentric chromosomal fragments. See Fig. 3. d, As in a. Genetically unmodified PDTO-9 organoid. Cells were stained with Syto 11 to allow single-cell picking. 85 out of 91 cells provided quality sequence (93% recovery).