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.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Requirements

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

Material

Lesson Slides Hands-on Recordings Input dataset Workflows
ATAC-Seq data analysis
DNA Methylation data analysis
Formation of the Super-Structures on the Inactive X
ChIP-seq
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
Identification of the binding sites of the Estrogen receptor
ChIP-seq work-in-progress
Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
ChIP-seq
Infinium Human Methylation BeadChip
Introduction to ChIP-Seq data analysis
Introduction to DNA Methylation data analysis

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.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Maintainers

This material is maintained by:

orcid logoAvatarLucille Delisleorcid logoAvatarFlorian HeylAvatarJoachim WolffAvatarDevon 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:

orcid logoAvatarAnika Erxlebenorcid logoAvatarLucille Delisleorcid logoAvatarFlorian Heylorcid logoAvatarMaria DoyleAvatarLeily Rabbaniorcid logoAvatarMo HeydarianAvatarJoachim Wolfforcid logoAvatarKrzysztof PoterlowiczAvatarFriederike DündarAvatarFidel Ramirezorcid logoAvatarYvan Le BrasAvatarVivek Bhardwajorcid logoAvatarBérénice BatutAvatarDevon RyanAvatarEkaterina PolkhAvatarKatarzyna Muratorcid logoAvatarMallory Freeberg