Systematic evaluation of factors influencing ChIP-seq fidelity

The authors analyze how sequencing depth, choice of control sample, paired-end versus single-end reads and the selection of peak-calling algorithm influence the interpretation of chromatin immunoprecipitation–sequencing (ChIP-seq) experiments. We evaluated how variations in sequencing depth and othe...

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Veröffentlicht in:	Nature methods 2012-06, Vol.9 (6), p.609-614
Hauptverfasser:	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
Format:	Artikel
Sprache:	eng
Schlagworte:	631/1647/2217/2088 631/1647/48 631/1647/514/2254 Algorithms Animals Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Chromatin Chromatin - chemistry Chromatin Immunoprecipitation - methods Chromatin Immunoprecipitation - standards DNA sequencing Drosophila melanogaster Drosophila Proteins - genetics False Positive Reactions Gene Library Genomes Genomics High-Throughput Nucleotide Sequencing Histone-Lysine N-Methyltransferase - genetics Insects Life Sciences Nucleotide sequencing Oligonucleotide Array Sequence Analysis Physiological aspects Proteomics Repressor Proteins - genetics Sensitivity and Specificity Transcription factors
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