DC Field | Value | Language |
---|---|---|
dc.contributor.author | KIM, TAE KYUNG | - |
dc.date.accessioned | 2018-12-04T01:55:13Z | - |
dc.date.available | 2018-12-04T01:55:13Z | - |
dc.date.created | 2018-11-21 | - |
dc.date.issued | 2012-06 | - |
dc.identifier.issn | 1548-7091 | - |
dc.identifier.uri | https://oasis.postech.ac.kr/handle/2014.oak/94321 | - |
dc.description.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. | - |
dc.language | English | - |
dc.publisher | NATURE PUBLISHING GROUP | - |
dc.relation.isPartOf | NATURE METHODS | - |
dc.title | Systematic evaluation of factors influencing ChIP-seq fidelity | - |
dc.type | Article | - |
dc.identifier.doi | 10.1038/NMETH.1985 | - |
dc.type.rims | ART | - |
dc.identifier.bibliographicCitation | NATURE METHODS, v.9, no.6, pp.609 - + | - |
dc.identifier.wosid | 000304778500029 | - |
dc.date.tcdate | 2019-02-01 | - |
dc.citation.endPage | + | - |
dc.citation.number | 6 | - |
dc.citation.startPage | 609 | - |
dc.citation.title | NATURE METHODS | - |
dc.citation.volume | 9 | - |
dc.contributor.affiliatedAuthor | KIM, TAE KYUNG | - |
dc.description.journalClass | 1 | - |
dc.description.journalClass | 1 | - |
dc.description.wostc | 84 | - |
dc.type.docType | Article | - |
dc.subject.keywordPlus | FACTOR-BINDING SITES | - |
dc.subject.keywordPlus | MODEL-BASED ANALYSIS | - |
dc.subject.keywordPlus | RNA-SEQ | - |
dc.subject.keywordPlus | GENOME | - |
dc.relation.journalWebOfScienceCategory | Biochemical Research Methods | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Biochemistry & Molecular Biology | - |
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