Epigenetics

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to ChIP-Seq data analysis
slides
Introduction to DNA Methylation data analysis
slides
ATAC-Seq data analysis
tutorial zenodo_link workflow
DNA Methylation data analysis
tutorial zenodo_link workflow interactive_tour
Formation of the Super-Structures on the Inactive X
slides tutorial zenodo_link workflow interactive_tour
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
tutorial zenodo_link workflow interactive_tour
Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
tutorial zenodo_link workflow interactive_tour
Infinium Human Methylation BeadChip
slides tutorial zenodo_link interactive_tour

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/epigenetics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Maintainers

This material is maintained by:

Joachim WolffJoachim Wolff, Devon RyanDevon Ryan

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Bérénice BatutBérénice Batut, Joachim WolffJoachim Wolff, Yvan Le BrasYvan Le Bras, Lucille DelisleLucille Delisle, Maria DoyleMaria Doyle, Florian HeylFlorian Heyl, Devon RyanDevon Ryan, Friederike DündarFriederike Dündar, Anika ErxlebenAnika Erxleben, Vivek BhardwajVivek Bhardwaj, Fidel RamirezFidel Ramirez, Leily RabbaniLeily Rabbani, Ekaterina PolkhEkaterina Polkh, Mallory FreebergMallory Freeberg, Mo HeydarianMo Heydarian, Katarzyna MuratKatarzyna Murat, Krzysztof PoterlowiczKrzysztof Poterlowicz