Systematic evaluation of factors influencing ChIP-seq fidelity
SCIE
SCOPUS
- Title
- Systematic evaluation of factors influencing ChIP-seq fidelity
- Authors
- KIM, TAE KYUNG
- Date Issued
- 2012-06
- Publisher
- NATURE PUBLISHING GROUP
- Abstract
- We evaluated how variations in sequencing depth and other parameters influence interpretation of chromatin immunoprecipitation-sequencing (ChIP-seq) experiments. Using Drosophila melanogaster S2 cells, we generated ChIP-seq data sets for a site-specific transcription factor (Suppressor of Hairy-wing) and a histone modification (H3K36me3). We detected a chromatin-state bias: open chromatin regions yielded higher coverage, which led to false positives if not corrected. This bias had a greater effect on detection specificity than any base-composition bias. Paired-end sequencing revealed that single-end data underestimated ChIP-library complexity at high coverage. Removal of reads originating at the same base reduced false-positives but had little effect on detection sensitivity. Even at mappable-genome coverage depth of similar to 1 read per base pair, similar to 1% of the narrow peaks detected on a tiling array were missed by ChIP-seq. Evaluation of widely used ChIP-seq analysis tools suggests that adjustments or algorithm improvements are required to handle data sets with deep coverage.
- URI
- https://oasis.postech.ac.kr/handle/2014.oak/94321
- DOI
- 10.1038/NMETH.1985
- ISSN
- 1548-7091
- Article Type
- Article
- Citation
- NATURE METHODS, vol. 9, no. 6, page. 609 - +, 2012-06
- Files in This Item:
- There are no files associated with this item.
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.