A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
Summary: CUT&RUN is a recently developed in situ chromatin profiling technique that enables high-resolution chromatin mapping and probing. Herein, we describe our adapted CUT&RUN protocol for transcription factors (TFs). Our protocol outlines all necessary steps for TF profiling including th...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-09-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166721004573 |
| _version_ | 1819132521848242176 |
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| author | Nikki Ruoxi Kong Li Chai Daniel Geoffrey Tenen Mahmoud Adel Bassal |
| author_facet | Nikki Ruoxi Kong Li Chai Daniel Geoffrey Tenen Mahmoud Adel Bassal |
| author_sort | Nikki Ruoxi Kong |
| collection | DOAJ |
| description | Summary: CUT&RUN is a recently developed in situ chromatin profiling technique that enables high-resolution chromatin mapping and probing. Herein, we describe our adapted CUT&RUN protocol for transcription factors (TFs). Our protocol outlines all necessary steps for TF profiling including the procedure to obtain proteinA-Mnase, while also outlining the bioinformatic pipeline steps required to process, analyze, and identify novel binding sites and sequences. Due to the small number of cells required, this method will allow the elucidation of cell context-dependent functions of many TFs.For details on the use and execution of this protocol, please refer to Kong et al. (2021). |
| first_indexed | 2024-12-22T09:32:44Z |
| format | Article |
| id | doaj.art-83420f7895484e379bf1e4d2c7df4d2b |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-12-22T09:32:44Z |
| publishDate | 2021-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-83420f7895484e379bf1e4d2c7df4d2b2022-12-21T18:30:53ZengElsevierSTAR Protocols2666-16672021-09-0123100750A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell linesNikki Ruoxi Kong0Li Chai1Daniel Geoffrey Tenen2Mahmoud Adel Bassal3Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USADepartment of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USAHarvard Stem Cell Institute, Boston, MA 02115, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, SingaporeHarvard Stem Cell Institute, Boston, MA 02115, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Corresponding authorSummary: CUT&RUN is a recently developed in situ chromatin profiling technique that enables high-resolution chromatin mapping and probing. Herein, we describe our adapted CUT&RUN protocol for transcription factors (TFs). Our protocol outlines all necessary steps for TF profiling including the procedure to obtain proteinA-Mnase, while also outlining the bioinformatic pipeline steps required to process, analyze, and identify novel binding sites and sequences. Due to the small number of cells required, this method will allow the elucidation of cell context-dependent functions of many TFs.For details on the use and execution of this protocol, please refer to Kong et al. (2021).http://www.sciencedirect.com/science/article/pii/S2666166721004573BioinformaticsSequence analysisCell BiologyCell separation/fractionationGenomicsSequencing |
| spellingShingle | Nikki Ruoxi Kong Li Chai Daniel Geoffrey Tenen Mahmoud Adel Bassal A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines STAR Protocols Bioinformatics Sequence analysis Cell Biology Cell separation/fractionation Genomics Sequencing |
| title | A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines |
| title_full | A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines |
| title_fullStr | A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines |
| title_full_unstemmed | A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines |
| title_short | A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines |
| title_sort | modified cut run protocol and analysis pipeline to identify transcription factor binding sites in human cell lines |
| topic | Bioinformatics Sequence analysis Cell Biology Cell separation/fractionation Genomics Sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2666166721004573 |
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