All of the analyzed real datasets are publicly available and the relevant GEO accession codes are included in the manuscript. All of the simulated and real data can be accessed through Code Ocean at the following URL: https://doi.org/10.24433/CO.9044782e-cb96-4733-8a4f-bf42c21399e6. cNMF code is available on Github https://github.com/dylkot/cNMF/ (copy archived at https://github.com/elifesciences-publications/cNMF).
Run cNMF on the Quadrato et al brain organoid data and analyze the cell-type identity programs (in particular the mesodermal programs) and the cell-cycle and hypoxia programs present in this data
Figures and calculations:
Supplementary figure 8a: K selection plot
Supplementary figure 8b: Replicate consensus plots before and after filtering
Figure 2a: heatmap of GEP usages per cell
Supplementary figure 9: Co-usage vs pearson correlation of the GEPs
Supplementary figure 11: GEP usage overlap with published clusters
Figure 2d: muscle cell marker genes
Figure 2e: activity GEP marker genes
Figure 2c: Gene-set enrichments
Figure 2g: hypoxia GEP usage by cell-type
Figure 2f: Cell cycle GEP usage by cell-type
Co-usage of the proliferative precursor and immature muscle GEPs calculation
Figure 2b: tSNE plot of GEP usage
Supplementary figure 10: tSNE of GEP usage with separate panels for activity GEPs