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bioRxiv · 10.1101/672220

siQ-ChIP:A reverse-engineered quantitative framework for ChIP-sequencing

Dickson, B.·Tiedemann, R. L.·Chomiak, A. A.·Vaughan, R. M.·Cornett, E. M.·Rothbart, S. B.
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Abstract

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a key technique for mapping the distribution and relative abundance of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes. There is a perceived challenge regarding the ability to quantitatively plot ChIP-seq data, and as such, approaches making use of exogenous additives, or \"spike-ins\" have recently been developed. Relying on the fact that the IP step of ChIP-seq is a competitive binding reaction, we present a quantitative framework for ChIP-seq analysis that circumvents the need to modify standard sample preparation pipelines with spike-in reagents. We also introduce a visualization technique that, when paired with our formal developments, produces a much more rich characterization of sequencing data.

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Dickson, B., Tiedemann, R. L., Chomiak, A. A., Vaughan, R. M., Cornett, E. M., Rothbart, S. B.. 2019-06-15. siQ-ChIP:A reverse-engineered quantitative framework for ChIP-sequencing. https://doi.org/10.1101/672220

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