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

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

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoLucille Delisle avatar Lucille Delisleorcid logoFlorian Heyl avatar Florian HeylJoachim Wolff avatar Joachim WolffDevon Ryan avatar Devon Ryan

Contributors

This material was contributed to by:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoAnika Erxleben avatar Anika ErxlebenLeily Rabbani avatar Leily RabbaniFriederike Dündar avatar Friederike DündarEkaterina Polkh avatar Ekaterina Polkhorcid logoLucille Delisle avatar Lucille DelisleFidel Ramirez avatar Fidel Ramirezorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamienieckaorcid logoKrzysztof Poterlowicz avatar Krzysztof PoterlowiczJoachim Wolff avatar Joachim Wolfforcid logoKhaled Jum'ah avatar Khaled Jum'ahorcid logoMo Heydarian avatar Mo Heydarianorcid logoHelena Rasche avatar Helena RascheDevon Ryan avatar Devon RyanVivek Bhardwaj avatar Vivek Bhardwajorcid logoMaria Doyle avatar Maria Doyleorcid logoFlorian Heyl avatar Florian Heylorcid logoMallory Freeberg avatar Mallory Freeberg

Funding

These individuals or organisations provided funding support for the development of this resource