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

This tutorial illustrates:

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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. 

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Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007). Genome-Wide Mapping of in Vivo Protein-DNA Interactions (Vol. 316). New York, NY: Science.