ChIP Next Generation Sequencing Analysis: Complete A to Z

Did you know that chromatin immunoprecipitation (ChIP) is one of the most commonly used techniques when assessing the effect of epigenetic modifications on gene expression and hence cell identity? Traditionally ChIP was combined with polymerase chain reaction (PCR), but with the advent of next-generation sequencing (NGS), a far more powerful way to study epigenetic modifications on a genome-wide level is through ChIP followed by sequencing (ChIPseq) which this course is about.

I’m Alexander Abdulkader Kheirallah, PhD and I’ll be your instructor in this course. I have a doctorate in bioinformatics and my project involved analysis of many ChIPseq datasets. My bioinformatic work has been published in peer-reviewed journals. I have worked as a bioinformatician at University of Cambridge and I am also a data scientist. After the success of my first course on RNAseq differential gene expression analysis, I’ve decided to take it further by condensing years of my experience in the form of a concise and practical course about epigenomics and ChIPseq data analysis. The ability to analyse big genomic data gives you a lot of opportunities at the intersection of biology, medicine and computer science.

What makes this course unique is that it combines thorough study of epigenetic biology with deep and practical analytical capabilities.

Not only you’ll gain epigenetic knowledge to aid your ChIPseq analysis endeavors but also you’ll be able to effectively manage your projects, assess their quality, and analyse. You’ll be provided with NGS ChIPseq data and I’ll walk you through the ChIPseq analysis step-by-step.

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The course is split into 11 sections culminating with a capstone project that you can add to your portfolio:

1. Introduction to the course

2. Epigenetics of gene expression: a thorough view of biology - Part 1

3. Epigenetics of gene expression: a thorough view of biology - Part 2

4. Epigenetics and environment

5. Laboratory techniques of epigenetics and introduction to functional studies

6. Canonical ChIPseq analysis workflow

7. Environment setup and ChIPseq project management

8. Quality assessment with FastQC

9. Alignment

10. Filtering

11. Peak calling

12. Your capstone project

By the end of this course you will:

• Be able to manage the working environment of your ChIPseq projects

• You'll be given a FREE access to ChIPseq-analysis-ready Docker containers

• You'll be given a FREE access to a whole chapter from a review paper worth $31.50

• Be able to evaluate the quality of ChIPseq sequencing data using FastQC

• Be able to perform alignment of reads to the genome using Bowtie2

• Be able to filter aligned reads based on criteria of your own choosing

• Be able to run MACS3 peak calling algorithm

• Understand the full ChIPseq analysis workflow

• Be able to use your epigenetic knowledge in order to aid interpretation of ChIP data

• Be able to use the principles of functional studies and epigenetic lab techniques

• Be able to explain the relationship between epigenetics and environment