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| Status |
Public on May 30, 2024 |
| Title |
CUT&TAG analysis of R-loops in Mcm8 knockout MEFs and CUT&TAG analysis of R-loops and MCM8-binding sites in HEK293 cells |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
To reveal the role of MCM8 in suppressing R-loop accumulation, we performed the CUT&TAG assay using the S9.6 antibody to map genome-wide R-loops in Mcm8 wildtype MEFs and Mcm8 knockout MEFs. We also conducted the CUT&TAG assay to detect genome-wide R-loops in Ddx5 downregulated MEFs by adenovirus infection and in control MEFs. To investigate the underlying molecular mechanism of MCM8 suppressing R-loops, we conducted the DNA sequencing of libraries from CUT&TAG assay using the antibody against FLAG in HEK293 cells transfected with FLAG-MCM8 plasmid and using the S9.6 antibody in HEK293 cells. Besides, an IgG control and control of RNH1 overexpression were included.
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| Overall design |
CUT&TAG-seq for R-loops using the S9.6 antibody in Mcm8 wildtype and MCM8 knockout MEFs. CUT&TAG-seq for R-loops using the S9.6 antibody in DDX5 downregulated MEFs and control MEFs. CUT&TAG-seq for R-loops using the S9.6 antibody in HEK293 cells with or without RNH1 overexpression. CUT&TAG-seq for MCM8-binding sites using the anti-FLAG antibody in HEK293 cells with or without FLAG-MCM8 overexpression.CUT&TAG-seq using the no-specific antibody IgG was used as a control.
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| Contributor(s) |
Wen C, Zhao S, Yang Y |
| Citation(s) |
38858601 |
| |
| Submission date |
Jan 27, 2024 |
| Last update date |
Aug 09, 2024 |
| Contact name |
Can xin Wen |
| E-mail(s) |
wcx12362379@outlook.com
|
| Organization name |
Shandong University
|
| Department |
Center for Reproductive Medicine
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| Street address |
44 West Wenhua Rd
|
| City |
Jinan |
| ZIP/Postal code |
250012 |
| Country |
China |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA1070001 |
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