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
Introduction to DNA Methylation data analysis
ATAC-Seq data analysis
DNA Methylation data analysis
EWAS data analysis of 450k data
Formation of the Super-Structures on the Inactive X
ChIP-seq
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

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

It will launch a flavored Galaxy instance available on http://localhost:8080.

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, Katarzyna MuratKatarzyna Murat, Krzysztof PoterlowiczKrzysztof Poterlowicz, Friederike DündarFriederike Dündar, Anika ErxlebenAnika Erxleben, Vivek BhardwajVivek Bhardwaj, Fidel RamirezFidel Ramirez, Leily RabbaniLeily Rabbani, Ekaterina PolkhEkaterina Polkh