PT - JOURNAL ARTICLE AU - Abhishek A Singh AU - Karianne Schuurman AU - Ekaterina Nevedomskaya AU - Suzan Stelloo AU - Simon Linder AU - Marjolein Droog AU - Yongsoo Kim AU - Joyce Sanders AU - Henk van der Poel AU - Andries M Bergman AU - Lodewyk FA Wessels AU - Wilbert Zwart TI - Optimized ChIP-seq method facilitates transcription factor profiling in human tumors AID - 10.26508/lsa.201800115 DP - 2019 Feb 01 TA - Life Science Alliance PG - e201800115 VI - 2 IP - 1 4099 - https://www.life-science-alliance.org/content/2/1/e201800115.short 4100 - https://www.life-science-alliance.org/content/2/1/e201800115.full SO - Life Sci. Alliance2019 Feb 01; 2 AB - 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.