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Systematic evaluation of factors influencing ChIP-seq fidelity using ultra-deep sequencing

experiment: Systematic evaluation of factors influencing ChIP-seq fidelity using ultra-deep sequencing project: Regulatory Elements in Drosophila PI: Kevin White Labs: Kevin White
Chromatin immunoprecipitation (ChIP) followed by massively parallel sequencing (ChIP-seq) has become the predominant technique for profiling genome-wide DNA-protein interactions and histone marks, and has been widely adopted in studying transcriptional and epigenetic regulation in various biomedical research areas. Owing to the improved throughput of new sequencing platforms and the rapid decline of sequencing cost, the sequencing coverage of ChIP-seq experiments has been steadily increasing. For example, it has become routine to acquire the data at the sequencing depth of ~60-80 million reads in human/mouse, while the depth of the ChIP-seq data generated before is typically ~10-20 million reads. However, we lack a systematic evaluation of factors inherent in data analysis or experimental methods that may influence the results of a ChIP-seq experiment, especially at deep sequencing coverage. To fill this gap, we generated ultra-deep sequencing datasets for genomic DNA (gDNA), chromatin input, the ChIP of a transcription factor, Suppressor of Hairy wing (Su(Hw)), and the ChIP of a broad histone mark (H3K36me3) from the Drosophila Melangaster S2 cells. The samples were sequenced at ~1 read/bp of mappable fly genome (~36x raw sequence coverage and corresponding to ~2.4 billion reads in human).