Abstract
BackgroundThe growth of sequencing-based Chromatin Immuno-Precipitation studies call for a more in-depth understanding of the nature of the technology and of the resultant data to reduce false positives and false negatives. Control libraries are typically constructed to complement such studies in order to mitigate the effect of systematic biases that might be present in the data. In this study, we explored multiple control libraries to obtain better understanding of what they truly represent.MethodologyFirst, we analyzed the genome-wide profiles of various sequencing-based libraries at a low resolution of 1 Mbp, and compared them with each other as well as against aCGH data. We found that copy number plays a major influence in both ChIP-enriched as well as control libraries. Following that, we inspected the repeat regions to assess the extent of mapping bias. Next, significantly tag-rich 5 kbp regions were identified and they were associated with various genomic landmarks. For instance, we discovered that gene boundaries were surprisingly enriched with sequenced tags. Further, profiles between different cell types were noticeably distinct although the cell types were somewhat related and similar.ConclusionsWe found that control libraries bear traces of systematic biases. The biases can be attributed to genomic copy number, inherent sequencing bias, plausible mapping ambiguity, and cell-type specific chromatin structure. Our results suggest careful analysis of control libraries can reveal promising biological insights.
Highlights
Sequencing-based Chromatin-Immunoprecipitation (ChIP) study has been rapidly gaining traction
We found that control libraries bear traces of systematic biases
The biases can be attributed to genomic copy number, inherent sequencing bias, plausible mapping ambiguity, and cell-type specific chromatin structure
Summary
Sequencing-based Chromatin-Immunoprecipitation (ChIP) study has been rapidly gaining traction. The goal of sequencing-based ChIP is to identify locations in the genome where TF-DNA interactions mostly likely occur. Such locations are expected to be enriched with the sequenced fragments. The growth of sequencing-based Chromatin Immuno-Precipitation studies call for a more in-depth understanding of the nature of the technology and of the resultant data to reduce false positives and false negatives. Control libraries are typically constructed to complement such studies in order to mitigate the effect of systematic biases that might be present in the data. We explored multiple control libraries to obtain better understanding of what they truly represent
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have