Print Email Facebook Twitter Optimized ChIP-seq method facilitates transcription factor profiling in human tumors Title Optimized ChIP-seq method facilitates transcription factor profiling in human tumors Author Singh, Abhishek A. (Netherlands Cancer Institute) Schuurman, Karianne (Netherlands Cancer Institute) Nevedomskaya, Ekaterina (Netherlands Cancer Institute) Stelloo, Suzan (Netherlands Cancer Institute) Linder, Simon (Netherlands Cancer Institute) Droog, Marjolein (Netherlands Cancer Institute) Kim, Yongsoo (Netherlands Cancer Institute) Sanders, Joyce (Netherlands Cancer Institute) van der Poel, Henk (Netherlands Cancer Institute) Bergman, Andries M. (Netherlands Cancer Institute) Wessels, L.F.A. (TU Delft Pattern Recognition and Bioinformatics; Netherlands Cancer Institute) Zwart, Wilbert (Netherlands Cancer Institute; Eindhoven University of Technology) Date 2019 Abstract Chromatin immunoprecipitation (ChIP)-seq analyses of transcription factors in clinical specimens are challenging due to the technical limitations and low quantities of starting material, often resulting in low enrichments and poor signal-to-noise ratio. Here, we present an optimized protocol for transcription factor ChIP-seq analyses in human tissue, yielding an ~100% success rate for all transcription factors analyzed. As proof of concept and to illustrate general applicability of the approach, human tissue from the breast, prostate, and endometrial cancers were analyzed. In addition to standard formaldehyde fixation, disuccinimidyl glutarate was included in the procedure, greatly increasing data quality. To illustrate the sensitivity of the optimized protocol, we provide high-quality ChIP-seq data for three independent factors (AR, FOXA1, and H3K27ac) from a single core needle prostate cancer biopsy specimen. In summary, double-cross-linking strongly improved transcription factor ChIP-seq quality on human tumor samples, further facilitating and enhancing translational research on limited amounts of tissue. To reference this document use: http://resolver.tudelft.nl/uuid:a2f8d1e9-a152-4da9-b345-b9012869e434 DOI https://doi.org/10.26508/lsa.201800115 Source Life Science Alliance, 2 (1), 1-12 Part of collection Institutional Repository Document type journal article Rights © 2019 Abhishek A. Singh, Karianne Schuurman, Ekaterina Nevedomskaya, Suzan Stelloo, Simon Linder, Marjolein Droog, Yongsoo Kim, Joyce Sanders, Henk van der Poel, Andries M. Bergman, L.F.A. Wessels, Wilbert Zwart Files PDF 50079952_e201800115.full.pd.pdf 2.64 MB Close viewer /islandora/object/uuid:a2f8d1e9-a152-4da9-b345-b9012869e434/datastream/OBJ/view