Last updated: 2022-04-05
Checks: 2 0
Knit directory: hesc-epigenomics/
This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 5c3a499. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: output/
Untracked files:
Untracked: data
Untracked: data_old/
Untracked: figures_data/
Unstaged changes:
Modified: analysis/fig_04_microscopy.Rmd
Deleted: data/meta/Kumar_2020_scaling_groups.csv
Deleted: data/meta/Kumar_2020_scalinginfo.csv
Deleted: data/meta/Kumar_2020_stats_summary.csv
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5c3a499 | C. Navarro | 2022-04-05 | wflow_publish(“./analysis/index.Rmd”) |
| html | 5eb1b01 | C. Navarro | 2022-02-04 | Build site. |
| Rmd | 21ed358 | C. Navarro | 2022-02-04 | Index update |
| html | d495eb3 | C. Navarro | 2021-09-10 | Build site. |
| 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. |
| Rmd | d7e28c0 | C. Navarro | 2021-07-09 | wflow_publish(“./analysis/index.Rmd”, verbose = T) |
| 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 |
| Rmd | eb48856 | cnluzon | 2021-02-08 | wflow_publish(“analysis/”) |
| 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/”) |
| html | 331f00c | cnluzon | 2021-02-03 | Build site. |
| 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. |
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 here.
Figure 6. Trajectory inference and gene expression dynamics for EZH2i treated naïve hESC. 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.
See GitHub repository for more information about software requirements. This website was generated using workflowr, an R package for science reproducibility.