@article {Singhe201800115, author = {Abhishek A Singh and Karianne Schuurman and Ekaterina Nevedomskaya and Suzan Stelloo and Simon Linder and Marjolein Droog and Yongsoo Kim and Joyce Sanders and Henk van der Poel and Andries M Bergman and Lodewyk FA Wessels and Wilbert Zwart}, title = {Optimized ChIP-seq method facilitates transcription factor profiling in human tumors}, volume = {2}, number = {1}, elocation-id = {e201800115}, year = {2019}, doi = {10.26508/lsa.201800115}, publisher = {Life Science Alliance}, 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.}, URL = {https://www.life-science-alliance.org/content/2/1/e201800115}, eprint = {https://www.life-science-alliance.org/content/2/1/e201800115.full.pdf}, journal = {Life Science Alliance} }