Last updated: 2022-02-04
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Knit directory: hesc-epigenomics/
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Supplementary code for publication. A large proportion of the figures shown in this publication can be obtained directly from values in the main tables.
Figure 1. Diffuse H3K27me3 and H2Aub cover the naïve pluripotent genome. Chromosome-wide H3K27me3 hypermethylation does not impact transcription from the naïve X chromosomes.
Figure 2. H3K27me3 is adaptive to gene expression changes between naïve and primed pluripotent states and contributes to repression of non-state specific genes.
Figure 3. PRC2 inhibition derepresses a naïve-specific subset of bivalent genes.
Figure 4. Loss of H3K27me3 in naïve hESCs activates trophectoderm gene expression programs.
Figure 5. Single-cell transcriptomic profiling of EZH2i treated naïve and primed cells. Code provided on the repository under code folder. Data can be browsed at: LINK
Figure 6. Trajectory inference and gene expression dynamics for EZH2i treated naïve hESCs. Code provided on the repository under code folder.
Raw data can be obtained at GEO database: GSE181244.
Main tables and analysis can be generated running this code. Primary processed and scaled bigWig files and metadata including a pre-generated version of such tables can be found here. They should be put under data/ in the same directory where the repository was cloned.
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