DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells

Code repository for the paper:

Andrea Lauria*, Guohua Meng*, Valentina Proserpio*, Stefania Rapelli*, Mara Maldotti, Isabelle Laurence Polignano, Francesca Anselmi, Chiara Levra Levron, Giacomo Donati, Danny Incarnato, Anna Krepelova, Francesco Neri, Ivan Molineris, Salvatore Oliviero, "DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells." Nat Commun 14, 367 (2023). https://doi.org/10.1038/s41467-023-35938-x

* = equal contribution.

Repository structure

The folder structure of the repository is organized in the following way:

.
├── figures
│   ├── fig_1
│   ├── fig_2
│   ├── fig_3
│   ├── fig_4
│   ├── fig_5
│   ├── fig_6
│   └── fig_7
├── README.md
└── share
    ├── bin
    ├── env
    └── src

where:

• figures: code to reproduce the results presented in the figures.
• share: code and conda environment files shared among the analyses.

Each figure folder is organized as follows, e.g. for fig_1:

figures/fig_1
├── bin
│   └── scrnaseq-get_scrna_obj.r -> ../src/scrnaseq-get_scrna_obj.r
├── data
├── env
│   └── rstudio_Rv4.0.3.yml -> ../../../share/env/rstudio_Rv4.0.3.yml
├── makefile
└── src
    ├── scrnaseq-get_scrna_obj.r
    ├── scrnaseq-pseudotime-monocle3.r
    ├── scrnaseq-seurat-cluster.r
    ├── scrnaseq-seurat-da-fisher.r
    ├── scrnaseq-seurat-standard.r
    ├── scrnaseq-test_branch_expression.r
    ├── scrnaseq-visualize_da-fisher.r
    └── scrnaseq-visualize-data.r

where:

• bin: executable scripts/tools.
• data: processed data files.
• env: conda environment files.
• makefile: makefile with rules to run the analysis.
• src: analysis scripts.

Data availability

Raw and processed sequencing data are available from the Gene Expression Omnibus (GEO) database under accession code GSE168415.

Used software

• STAR 2.7.1a: https://github.com/alexdobin/STAR
• HISAT2 v2.2.1: http://daehwankimlab.github.io/hisat2/
• featureCounts v1.6.4: https://subread.sourceforge.net/
• Bismark v0.22.3: https://www.bioinformatics.babraham.ac.uk/projects/bismark/
• Bowtie2 v2.3.5: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
• bedtools v2.29.2: https://bedtools.readthedocs.io/en/latest/
• deepTools v3.3.1: https://deeptools.readthedocs.io/en/develop/
• MACS2 v2.2.5: https://pypi.org/project/MACS2/
• R v3.5.3, v3.6.1, v4.0.3: https://www.r-project.org/
• Seurat v4.0.0: https://satijalab.org/seurat/index.html
• Monocle3 v1.0.0: https://cole-trapnell-lab.github.io/monocle3/
• edgeR v3.32.1: https://bioconductor.org/packages/release/bioc/html/edgeR.html
• DSS v2.34.0: https://bioconductor.org/packages/release/bioc/html/DSS.html
• MethylKit v1.16.1: https://www.bioconductor.org/packages/release/bioc/html/methylKit.html

Additional sofware required for the analysis

• ngsRtools: https://github.com/andrealauria104/ngsRtools
• epigeNGS-pipe: https://github.com/andrealauria104/epigeNGS-pipe