Chromatin Immunoprecipitation Sequencing (ChIP-Seq) uses high-throughput DNA sequencing to map protein-DNA interactions across the entire genome. Partek^® Genomics Suite^® offers convenient visualization and analysis of ChIP-Seq data.

In this tutorial, we will use the Partek Genomics Suite ChIP-Seq workflow to analyze aligned data (.bam format) from a .

This tutorial illustrates:

Note: the workflow described is specific for PGS version 6.6. To upgrade to this version, go to the Main menu and access Help > Check for Updates. The screenshots shown below may vary slightly across hardware platforms and across different versions of PGS.

Description of the data set

The data for this tutorial comes from Johnson et al. (Science 2007), which first described the ChIP-Seq technique. This study mapped genomic binding sites for neuron-restrictive silencer factor (NRSF) transcription factor across the genome. There are two samples: an NRSF-enriched ChIP sample (chip.bam) and a control sample of input DNA without antibody immunoenrichment (mock.bam). The chip.bam file contains ~1.7 million mapped reads and the mock.bam file contains ~2.3 million mapped reads. These .bam files contain the aligned genomic locations and sequences of all mapped reads. This data set contains reads from a single-end (SE) library; the differences in processing paired-end (PE) reads will be discussed when applicable. 

Data for this tutorial can be downloaded from the Partek website at this link - ChIP-Seq tutorial data - or by going to the Next Generation Sequencing tab after selecting Help then On-line Tutorials from the Partek Genomics Suite main toolbar. 

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