ChIP-seq is a new approach for investigating entire transcription factor-DNA interactomes. ChIP-seq is comprised of chromatin immunoprecipitation (ChIP) followed by single-molecule-based sequencing (seq). ChIP-seq avoids the complications of array hybridization.
This track shows 25mer sequence reads obtained via a ChIP-seq protocol from samples enriched for a variety of transcription factors and a companion control sample of the same fixed chromatin without immuno-enrichment. These sequence reads were later analyzed using a peak locator to identify transcription factor positive binding events.
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Libraries were prepared from the ChIP DNA using the ligation mediated PCR Solexa protocol. The Solexa library construction protocol was modified to include a PCR preamplification following linker ligation and preceding gel electrophoresis. Reducing the size and narrowing the size range of DNAs collected from gel purification is intended to improve positional resolution of ChIP-seq. Reads which mapped to multiple genomic locations are not included. Up to two mismatches were allowed.
Myers Group: David Johnson, Betsy Anton, Loan Nguyen, Cat Medina, Richard Myers.
Wold Group: Barbara Wold, Ali Mortazavi, Kenneth McCue.
Solexa/Illumina Sequencing: Gary Schroth.
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