H3K27me3 hESC Epigenomics data

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Last updated: 2021-09-10

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Knit directory: hesc-epigenomics/

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File	Version	Author	Date	Message
Rmd	909edd6	C. Navarro	2021-09-10	wflow_publish(“./analysis/index.Rmd”)
html	8363fcf	C. Navarro	2021-07-09	Build site.
html	87db6b2	C. Navarro	2021-07-09	Build site.
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html	ce48d0f	C. Navarro	2021-07-08	Build site.
Rmd	2d5c9aa	C. Navarro	2021-07-08	wflow_publish(“./analysis/index.Rmd”, verbose = T)
html	9e8b1a9	cnluzon	2021-05-26	Metadata folder added
Rmd	0f37941	cnluzon	2021-03-12	Fig1 fresh
html	0f37941	cnluzon	2021-03-12	Fig1 fresh
Rmd	ef20c53	cnluzon	2021-03-11	Annotations
html	ef20c53	cnluzon	2021-03-11	Annotations
html	aa434ad	cnluzon	2021-02-08	Per chromosome density report
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html	0437358	cnluzon	2021-02-07	Build site.
Rmd	8942fdf	cnluzon	2021-02-07	Index page
html	8942fdf	cnluzon	2021-02-07	Index page
Rmd	0481b52	cnluzon	2021-02-05	RNA seq first analysis
html	0481b52	cnluzon	2021-02-05	RNA seq first analysis
Rmd	87ff15f	cnluzon	2021-02-05	Renamed read counts file
html	87ff15f	cnluzon	2021-02-05	Renamed read counts file
html	7cafaa1	cnluzon	2021-02-03	Build site.
Rmd	930c015	cnluzon	2021-02-03	wflow_publish(“analysis/”)
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Rmd	04408d2	cnluzon	2021-02-03	Global read counts
Rmd	897ecf5	cnluzon	2021-02-02	wflow_git_commit(all = TRUE)
Rmd	407fa20	cnluzon	2021-02-02	Start workflowr project.

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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.

Upon publication, a link to a comprehensive set of files, including bigWig files, will be provided.

Main tables and analysis can be generated running this code.

See GitHub repository for more information about software requirements. This website was generated using workflowr, an R package for science reproducibility.

Publication figures

• Figure 1. High levels of H3K27m3 and H2AUb broadly cover the naïve pluripotent genome.
• Figure 2. X chromosome in naïve hESCs accumulate exceptional amounts of H3K27m3 without a globally repressive function.
• Figure 3. H3K27m3 is adaptive to gene expression changes between naïve and primed pluripotent state and contributes to repression of non-state specific genes.
• Figure 4. Loss of H3K27m3 in naïve hESCs derepresses a set of genes that drive hESCs towards a rare naturally ocurring intermediate pluripotent state.
• Figure 5. Loss of H3K27m3 in naïve hESCs activates trophectoderm and placental gene expression programs.

Supplementary data and analyses

• Master gene table. Notebook with the code that generates the master gene table.
• Master bins table. Notebook with the code that generates the master bins table.
• Replicates analysis. Notebook with some figures showing replicates data.

Main data files

• Gene table. Contains histone mark values across 5kb regions around gene TSS in the hg38 genome, RNA-seq plus statistics on differentially decorated promoters and differentially expressed genes across conditions. Extra annotations on Court 2017 bivalency, lineage marker genes and H3K27m3 bivalency group are added.
• Bins table. Gathers histone mark values across 10kb windows in the hg38 genome, plus statistics on differentially decorated regions across conditions.