RT Journal Article
SR Electronic
T1 Ultra-parallel ChIP-seq by barcoding of intact nuclei
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 276469
DO 10.1101/276469
A1 L. Arrigoni
A1 H. Al-Hasani
A1 F. Ramírez
A1 I. Panzeri
A1 D.P Ryan
A1 D. Santacruz
A1 N. Kress
A1 A. Pospisilik
A1 U. Böenisch
A1 T. Manke
YR 2018
UL http://biorxiv.org/content/early/2018/03/05/276469.abstract
AB 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.