TY - JOUR
T1 - Optimized ChIP-seq method facilitates transcription factor profiling in human tumors
AU - Singh, Abhishek A.
AU - Schuurman, Karianne
AU - Nevedomskaya, Ekaterina
AU - Stelloo, Suzan
AU - Linder, Simon
AU - Droog, Marjolein
AU - Kim, Yongsoo
AU - Sanders, Joyce
AU - van der Poel, Henk
AU - Bergman, Andries M.
AU - Wessels, Lodewyk F.A.
AU - Zwart, Wilbert
PY - 2019
Y1 - 2019
N2 - 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.
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.
UR - http://www.scopus.com/inward/record.url?scp=85059891142&partnerID=8YFLogxK
U2 - 10.26508/lsa.201800115
DO - 10.26508/lsa.201800115
M3 - Article
AN - SCOPUS:85059891142
SN - 2575-1077
VL - 2
SP - 1
EP - 12
JO - Life Science Alliance
JF - Life Science Alliance
IS - 1
M1 - e201800115
ER -