@article{1926977abafd483284f61cb9ac880461,
title = "High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro",
abstract = "High-throughput sequencing SELEX (HT-SELEX) is a powerful technique for unbiased determination of preferred target motifs of DNA-binding proteins in vitro. The procedure depends upon selection of DNA binding sites from a random library of oligonucleotides by purifying protein-DNA complexes and amplifying bound DNA using the polymerase chain reaction. Here, we describe an optimized step-by-step protocol for HT-SELEX compatible with Illumina sequencing. We also introduce a bioinformatic pipeline (eme_selex) facilitating the detection of promiscuous DNA binding by analyzing the enrichment of all possible k-mers. For complete details on the use and execution of this protocol, please refer to Pantier et al. (2021).",
keywords = "bioinformatics, high throughput screening, molecular biology, sequence analysis, sequencing",
author = "Rapha{\"e}l Pantier and Kashyap Chhatbar and Grace Alston and Lee, {Heng Yang} and Adrian Bird",
note = "Funding Information: We thank Arttu Jolma and Jussi Taipale for useful advice regarding HT-SELEX library design. We thank Vladimir Benes and the EMBL Genecore Facility for technical support with high-throughput sequencing and library design. This work was funded by European Research Council Advanced Grant EC 694295 Gen-Epix and Wellcome Investigator Award 107930 to A.B., who is also a member of the Simons Initiative for the Developing Brain. The Centre for Cell Biology is supported by core grant 203149 from Wellcome . This work was supported by the Edinburgh Protein Production Facility (EPPF) and the Centre Core Grants ( 092076 and 203149 ) to the Wellcome Centre for Cell Biology at the University of Edinburgh . Publisher Copyright: {\textcopyright} 2022 The Author(s)",
year = "2022",
month = sep,
day = "16",
doi = "10.1016/j.xpro.2022.101490",
language = "English",
volume = "3",
journal = "STAR Protocols",
issn = "2666-1667",
publisher = "Cell Press",
number = "3",
}