Person: He, Housheng H
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Housheng H
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He, Housheng H
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Publication Systematic Evaluation of Factors Influencing ChIP-Seq Fidelity(Nature Publishing Group, 2012) Negre, Nicolas; Li, Qunhua; Mieczkowska, Joanna O.; Slattery, Matthew; Kim, Tae-Kyung; Zieba, Jennifer; Ruan, Yijun; Bickel, Peter J.; Wold, Barbara J.; Lieb, Jason D.; Chen, Yiwen; Liu, Tao; Zhang, Yong; He, Housheng H; Myers, Richard M.; White, Kevin P.; Liu, XiaoleWe 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.Publication Polycomb-independent activity of EZH2 in castration resistant prostate cancer(BioMed Central, 2013) Xu, Kexin; Wu, Zhenhua; Groner, Anna Claire; He, Housheng H; Cai, Changmeng; Stack, Edward C; Loda, Massimo; Liu, Tao; Morrissey, Colm; Vessella, Robert L; Kantoff, Philip; Balk, Steven; Liu, Xiaole; Brown, MylesPublication A closer look into DNase I hypersensitivity(BioMed Central, 2013) He, Housheng H; Meyer, Clifford; Long, Henry; Liu, Xiaole; Brown, Myles