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Systematic evaluation of factors influencing ChIP-seq fidelity
We performed a systematic evaluation of how variations in sequencing depth and other parameters influence interpretation of Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) experiments. Using Drosophila S2 cells, we generated ChIP-seq datasets for a site-specific transcription...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477507/ https://www.ncbi.nlm.nih.gov/pubmed/22522655 http://dx.doi.org/10.1038/nmeth.1985 |
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author | Chen, Yiwen Negre, Nicolas Li, Qunhua Mieczkowska, Joanna O. Slattery, Matthew Liu, Tao Zhang, Yong Kim, Tae-Kyung He, Housheng Hansen Zieba, Jennifer Ruan, Yijun Bickel, Peter J. Myers, Richard M. Wold, Barbara J. White, Kevin P. Lieb, Jason D. Liu, X. Shirley |
author_facet | Chen, Yiwen Negre, Nicolas Li, Qunhua Mieczkowska, Joanna O. Slattery, Matthew Liu, Tao Zhang, Yong Kim, Tae-Kyung He, Housheng Hansen Zieba, Jennifer Ruan, Yijun Bickel, Peter J. Myers, Richard M. Wold, Barbara J. White, Kevin P. Lieb, Jason D. Liu, X. Shirley |
author_sort | Chen, Yiwen |
collection | PubMed |
description | We performed a systematic evaluation of how variations in sequencing depth and other parameters influence interpretation of Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) experiments. Using Drosophila S2 cells, we generated ChIP-seq datasets 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 and 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. The removal of reads originating at the same base reduced false-positives while having little effect on detection sensitivity. Even at a depth of ~1 read/bp coverage of mappable genome, ~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 datasets with deep coverage. |
format | Online Article Text |
id | pubmed-3477507 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
record_format | MEDLINE/PubMed |
spelling | pubmed-34775072012-12-01 Systematic evaluation of factors influencing ChIP-seq fidelity Chen, Yiwen Negre, Nicolas Li, Qunhua Mieczkowska, Joanna O. Slattery, Matthew Liu, Tao Zhang, Yong Kim, Tae-Kyung He, Housheng Hansen Zieba, Jennifer Ruan, Yijun Bickel, Peter J. Myers, Richard M. Wold, Barbara J. White, Kevin P. Lieb, Jason D. Liu, X. Shirley Nat Methods Article We performed a systematic evaluation of how variations in sequencing depth and other parameters influence interpretation of Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) experiments. Using Drosophila S2 cells, we generated ChIP-seq datasets 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 and 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. The removal of reads originating at the same base reduced false-positives while having little effect on detection sensitivity. Even at a depth of ~1 read/bp coverage of mappable genome, ~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 datasets with deep coverage. 2012-04-22 2012-06 /pmc/articles/PMC3477507/ /pubmed/22522655 http://dx.doi.org/10.1038/nmeth.1985 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms |
spellingShingle | Article Chen, Yiwen Negre, Nicolas Li, Qunhua Mieczkowska, Joanna O. Slattery, Matthew Liu, Tao Zhang, Yong Kim, Tae-Kyung He, Housheng Hansen Zieba, Jennifer Ruan, Yijun Bickel, Peter J. Myers, Richard M. Wold, Barbara J. White, Kevin P. Lieb, Jason D. Liu, X. Shirley Systematic evaluation of factors influencing ChIP-seq fidelity |
title | Systematic evaluation of factors influencing ChIP-seq fidelity |
title_full | Systematic evaluation of factors influencing ChIP-seq fidelity |
title_fullStr | Systematic evaluation of factors influencing ChIP-seq fidelity |
title_full_unstemmed | Systematic evaluation of factors influencing ChIP-seq fidelity |
title_short | Systematic evaluation of factors influencing ChIP-seq fidelity |
title_sort | systematic evaluation of factors influencing chip-seq fidelity |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477507/ https://www.ncbi.nlm.nih.gov/pubmed/22522655 http://dx.doi.org/10.1038/nmeth.1985 |
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