Supplementary data 1. TF ChIP-seq peaks, motif enrichment and HDMB03/MB3W1 bulk-RNA-seq data

## ChIP-seq analysis 1. Individual peak summits. Each peak summit was extended to a 100bp window aroung the summit,filtered for non-canonical chromosomes and black-listed regions. MB129_CRX_summits.fil.ext.bedMB129_EOMES_summits.fil.ext.bedMB129_PAX6_summits.fil.ext.bedMB165_EOMES_summits.fil.ext.bedMB297_CRX_summits.fil.ext.bedMB297_EOMES_summits.fil.ext.bedMB96_CRX_summits.fil.ext.bed 2. Merged peak summits per TF.Peak summits from multiple samples were merged to obtain consensus peak summits. This data was used as input for HOMER motif enrichment analysis CRX.com.bedEOMES.com.bedPAX6.bed 3. Overlap of peak summits between consensus EOMES and CRX binding sites.EOMES_CRX.ov.bed 4. HOMER output foldersCRXEOMESPAX6 5. MEME motif analysis reports ## HDMB03 and MB3W1 cell line and PDX RNA-seq 6. Gene count matricesCell line:HDMB03_CL_mat.txtMB3W1_CL_mat.txtPDX:HDMB03_PDX_mat.txtMB3W1_PDX_mat.txt 7. Metadata excel fileHDMB03 and MB3W1 RNA-seq metadata.xlsx