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Abstract / Description of output
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).
Original language | English |
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Article number | 101490 |
Number of pages | 21 |
Journal | Star Protocols |
Volume | 3 |
Issue number | 3 |
Early online date | 22 Jun 2022 |
DOIs | |
Publication status | Published - 16 Sept 2022 |
Keywords / Materials (for Non-textual outputs)
- bioinformatics
- high throughput screening
- molecular biology
- sequence analysis
- sequencing