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. 2024 Mar 6;628(8007):373–380. doi: 10.1038/s41586-024-07128-2

Extended Data Fig. 9. mESC sequencing assays compared to public genomic data.

Extended Data Fig. 9

a, Snapshot of a region on M. musculus chromosome 3 showing sequencing data for ATAC-seq/DNase-seq, H3K4me3 ChIP-seq, H3K27ac ChIP-seq, H3K27me3 ChIP-seq, RNAP2 ChIP-seq, and RNA-seq, from this study (purple) and from publicly available, published datasets (grey). Data from this study is from one replicate mESC clone with HPRT1 integrated on chrX. b, ENCODE data for DNase-seq, H3K4me3, RNAP2, H3K27ac, and H3K27me3 ChIP-seq, and RNA-seq from mouse embryonic stem cells. The browser shot shows the region on chrX used for integration of synthetic loci, including the native mouse Hprt gene. Predicted CpG islands are shown below. c, Data from this study for a clone in which HPRT1R in integrated on chromosome 3 (HPRT1R chr3 (1)) and so has an intact Hprt locus. d, ENCODE data for DNase-seq, H3K4me3, H3K27ac, and H3K27me3 ChiP-seq, and RNA-seq from the H1 human embryonic stem cell line. Browser shot is from the hg38 genome and shows the region on human chrX containing the native HPRT1 gene. Predicted CpG islands are shown below. The region that was cloned as the synthetic HPRT1 locus is indicated with a grey bar. Mouse datasets are: DNase-seq from ES-E14 mouse embryonic stem cells, ENCSR000CMW. ChIP-seq from ES-Bruce mouse embryonic stem cells, ENCSR000CBG, ENCSR000CDE, ENCSR000CFN, ENCSR000CCC. RNA-seq from ES-E14 mouse embryonic stem cells, ENCSR000CWC. Human datasets are: DNase-seq from H1-hESC ENCSR000EJN, ChIP-seq from H1-hESC ENCSR443YAS, ENCSR880SUY, ENCSR928HYM, RNA-seq from H1-hESC ENCSR000COU.