TY - JOUR T1 - Ultra-parallel ChIP-seq by barcoding of intact nuclei JF - bioRxiv DO - 10.1101/276469 SP - 276469 AU - L. Arrigoni AU - H. Al-Hasani AU - F. Ramírez AU - I. Panzeri AU - D.P Ryan AU - D. Santacruz AU - N. Kress AU - A. Pospisilik AU - U. Böenisch AU - T. Manke Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/03/05/276469.abstract N2 - Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. However, sample preparation is still a largely individual and labor-intensive process that hinders assay throughput and comparability. Here, we present a novel method for ultra-parallelized high-throughput ChIP-seq that addresses the aforementioned problems. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), employs barcoding of chromatin within intact nuclei extracted from different sources (e.g. tissues, treatments, time points). Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and significant workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation large-scale clinical studies and scarce samples. RELACS can generate ChIP-seq libraries from hundreds of samples within three days and with less than 1000 cells per sample. ER -