ChIP-seq lab (Developmental Systems I 2019)
The goal of this session is to teach you how to design a ChIP-seq experiment, perform the experiment, analyze the data, and interpret the data. There will be no bench work involved, we will go through the experimental set up and controls during our meeting. The lab component is a take-home project, involving analysis of a ChIP-seq data set and finding a DNA sequence motif. You should start the project a week earlier.
1 Week prior to the class:
Watch the ChIP-seq analysis Workshop.
Download the SDC-2 ChIP-seq data and Input-seq data. Note that these are large files.
Analyze the data (QC, align, MACS, motif finding) using Galaxy. You can use the following videos to guide you through the process:
Print out the first page including motif logos from MEME ChIP, label with your name, and bring to class.
**** Work in groups if you would like. If you cannot go through the analysis, bring in your questions to the Friday's meeting, try again the following week, and email me the logo the following Friday.
note: if you are already familiar with sequencing data analysis and use HPC, commandline, R and able to write your own scripts, skip the take home project. This project is designed to empower biologists who want to learn data analysis.