Workshop Introduction
Welcome! This workshop has been created as part of the Unimi course “Molecular Biology applied to Biotechnology”. The aim is to introduce you to the world of bioinformatics and to some of the most important concepts related to the analysis of Next Generation Sequencing (NGS) data.
In particular, you will be guided through the main steps of a ChIP-seq experiment, starting from the experimental design and its major challenges and then diving into a ChIP-seq analysis workflow! The hands-on part is based on R and for this reason an essential introduction to this programming language will be provided as well.
The dataset used in this workshop is taken from our study published on Nature Communications on 2021, “Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ”. Part of the adventure will be dedicated to trying to reproduce some relevant analyses and plots published as results!
Learning Objectives
- Get an overview of the ChIP-seq assay and its significance in genomic research
- Understand applications and key insights derived from ChIP-seq experiments
- Familiarize with basic R functionalities
- Describe the core steps of a ChIP-seq data analysis pipeline
- Learn how to navigate and utilize public resources for the analysis and exploration of genomic data
Workshop Schedule
This workshop is intended as a three-day tutorial. Each day will be dedicated to specific activities:
Day 1
- Introduction to ChIP-seq
- Setting up R environment
- Understanding ChIP-seq (and NGS) data core processing
- Dataset introduction and exploration
Day 2
- Data normalization with
edgeR - Diagnostic and exploratory analysis
- Differential analysis for ChiP-seq data
- Visualization of the results
Day 3
- Downstream analyses on interesting subset of data, including:
- Gene ontology with
gProfiler - Motif Analysis with
MEME
- Gene ontology with
- Exploration of publicly available resources for accessing genomic data
Us
🧑🔬 Jacopo Arrigoni (jacopo.arrigoni@ifom.eu)
👩💻 Carolina Dossena (carolina.dossena@ifom.eu)
Credits
This workshop was inspired by other tutorials on ChIP-seq data analysis (the Bioconductor course, the teaching material from the HBC training and the tutorial from UCR. For the R fundamentals part look at this R book for beginners. Mattia Toninelli (mattia.toninelli@ifom.eu) helped with the development of this site and some course sections. The design of the analyses and the codes have been generated together with Michaela Fakiola (michaela.fakiola@ifom.eu).
License
All of the material in this course is under a Creative Commons Attribution license (CC BY 4.0) which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.