Introduction to NGS Tech and ChIP-seq
June 21, 2013
Biostatistics and Bioinformatics Short Course
Presented by James Ward
Time: 1:00 PM - 2:30 PM
Room: NIEHS Rall 101A
Abstract: We will start by looking at the evolution of sequencing technology and briefly go over the chemistry and principles behind first, second, and third generation sequencers. We will then delve into the methods and applications for ChIP-seq analysis. ChIP-Seq stands for Chromatin Immunoprecipitation followed by Sequencing, and as the name suggests, uses immunoprecipitation to assess the genomic loci of DNA binding proteins such as transcription factors, histone modifications, CTCF etc. This section will include an overview of the ChIP-seq protocol, experimental requirements, statistical analyses, data formats and visualization. We will end with a demonstration of ChIP-seq data analysis, starting with raw data from the sequencer to the visualization of “Chipped” peaks in the UCSC genome browser. Please note that due to time limitations, we will not be able to perform a real-time demonstration and will instead rely on a recently analyzed example. Bringing a laptop is not necessary.