An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactions
Summary: Genome-wide mapping of transcription factors (TFs) is critical to understand their functions. In chromatin immunoprecipitation (ChIP)-seq assay, it’s challenging to study recruitment of low-abundant TFs transiently boud to the genome. Here, we present an optimized protocol using ChIP Next-G...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-12-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722007985 |
| _version_ | 1798005534968774656 |
|---|---|
| author | Fang Tao Egidy Rhonda Xi He John M. Perry Linheng Li |
| author_facet | Fang Tao Egidy Rhonda Xi He John M. Perry Linheng Li |
| author_sort | Fang Tao |
| collection | DOAJ |
| description | Summary: Genome-wide mapping of transcription factors (TFs) is critical to understand their functions. In chromatin immunoprecipitation (ChIP)-seq assay, it’s challenging to study recruitment of low-abundant TFs transiently boud to the genome. Here, we present an optimized protocol using ChIP Next-Gen Seq Sepharose (Staph-seq) to efficiently pull down chromatin complexes. The double size selection promotes sensitive capture of genome-wide protein-DNA associations while eliminating potential Staph A contamination, which is a common problem in protocols using Staph A cells.For complete details on the use and execution of this protocol, please refer to Tao et al. (2020).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-11T12:40:49Z |
| format | Article |
| id | doaj.art-42c260d40ab4412a98ae11e206d6fa94 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-11T12:40:49Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-42c260d40ab4412a98ae11e206d6fa942022-12-22T04:23:30ZengElsevierSTAR Protocols2666-16672022-12-0134101918An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactionsFang Tao0Egidy Rhonda1Xi He2John M. Perry3Linheng Li4Children’s Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA; Stowers Institute for Medical Research, Kansas City, MO 64111, USA; Corresponding authorStowers Institute for Medical Research, Kansas City, MO 64111, USAStowers Institute for Medical Research, Kansas City, MO 64111, USAChildren’s Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USAStowers Institute for Medical Research, Kansas City, MO 64111, USA; Corresponding authorSummary: Genome-wide mapping of transcription factors (TFs) is critical to understand their functions. In chromatin immunoprecipitation (ChIP)-seq assay, it’s challenging to study recruitment of low-abundant TFs transiently boud to the genome. Here, we present an optimized protocol using ChIP Next-Gen Seq Sepharose (Staph-seq) to efficiently pull down chromatin complexes. The double size selection promotes sensitive capture of genome-wide protein-DNA associations while eliminating potential Staph A contamination, which is a common problem in protocols using Staph A cells.For complete details on the use and execution of this protocol, please refer to Tao et al. (2020).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722007985High Throughput ScreeningMolecular BiologyChromatin immunoprecipitation (ChIP) |
| spellingShingle | Fang Tao Egidy Rhonda Xi He John M. Perry Linheng Li An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactions STAR Protocols High Throughput Screening Molecular Biology Chromatin immunoprecipitation (ChIP) |
| title | An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactions |
| title_full | An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactions |
| title_fullStr | An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactions |
| title_full_unstemmed | An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactions |
| title_short | An optimized chromatin immunoprecipitation protocol using Staph-seq for analyzing genome-wide protein-DNA interactions |
| title_sort | optimized chromatin immunoprecipitation protocol using staph seq for analyzing genome wide protein dna interactions |
| topic | High Throughput Screening Molecular Biology Chromatin immunoprecipitation (ChIP) |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722007985 |
| work_keys_str_mv | AT fangtao anoptimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT egidyrhonda anoptimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT xihe anoptimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT johnmperry anoptimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT linhengli anoptimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT fangtao optimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT egidyrhonda optimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT xihe optimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT johnmperry optimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions AT linhengli optimizedchromatinimmunoprecipitationprotocolusingstaphseqforanalyzinggenomewideproteindnainteractions |