Figure EV3. SOX2 and SOX9 knock‐down resulted in different transcriptome changes.

1. Unsupervised hierarchical clustering of non‐targeting control, SOX2 knock‐down and SOX9 knock‐down RNA‐Seq results.
2. Venn diagram showing minimal overlap of differentially expressed genes after SOX2 knock‐down in two different parental organoid lines. Overlapping DE genes were labelled in boxes.
3. qPCR of selected DE genes from SOX9 RNA‐seq data following SOX9 knock‐down in a further 2 independent organoid lines. Cells harvested 5 days after knock‐down. Error bars: mean ± SEM. Statistical analysis was using the two‐tailed paired t‐test. P‐values are reported as follows: **P < 0.01, ***P < 0.001. N = 3 bio‐replicates (Organoid line BRC2174 with two different NT gRNAs and two different SOX9 gRNAs, and Organoid line BRC2136 with 1 NT gRNA and 1 SOX9 gRNA) were used.
4. Sashimi plot to visualise splicing junction of NT control and SOX9 KD. Upper panel: Sashimi plot was used to visualise splicing junction information in non‐targeting gRNA control and SOX9 knock‐down groups. Junctional reads between intron #1 and exon #2 were only observed in SOX9 knock‐down groups and not in non‐targeting gRNA control groups. Lower panel: major SOX9 domains in relation to the SOX9 genomic locus. Exon #1 contains DIM and part of the HMG domain. DIM, dimerization domain. HMG, high‐mobility group domain. PQA, proline‐glutamine‐alanine repeats domain. TA, transactivation domain.
5. Heatmap of gene expression from representative GO terms: cell division and small molecule metabolism together with gene expression of upregulated non‐lung lineage genes. OL, organoid line.
6. Selected GO enrichment in DE genes after SOX9 knock‐down.

Source data are available online for this figure.