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Systematic evaluation of factors influencing ChIP-seq fidelity
Open accessAbstract
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 ∼1 read per base pair, ∼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.
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Self-citationTandem repeats finder: a program to analyze DNA sequences
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
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H3K4me3 breadth is linked to cell identity and transcriptional consistency
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Mammalian heat shock response and mechanisms underlying its genome-wide transcriptional regulation
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Metadata
- Authors
- Chen, Y., Negre, N., Li, Q., Mieczkowska, J. O., Slattery, M., Liu, T., Zhang, Y., Kim, T.-K., He, H. H., Zieba, J., Ruan, Y., Bickel, P. J., Myers, R. M., Wold, B. J., White, K. P., Lieb, J. D., & Liu, X. S.
- Venue
- Nature Methods
- Published
- 2012-04-22
- Volume
- 9
- Issue
- 6
- Pages
- 609-614
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2146303939
- Cited by
- 171
- References
- 5
- FWCI
- 8.25
- Type
- journal article
- Language
- en
- Open access
- green
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- Chen, Y., Negre, N., Li, Q., Mieczkowska, J. O., Slattery, M., Liu, T., Zhang, Y., Kim, T.-K., He, H. H., Zieba, J., Ruan, Y., Bickel, P. J., Myers, R. M., Wold, B. J., White, K. P., Lieb, J. D., & Liu, X. S. (2012). Systematic evaluation of factors influencing ChIP-seq fidelity. Nature Methods. https://doi.org/10.1038/nmeth.1985
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