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Series GSE254352 Query DataSets for GSE254352
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.
 
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.
 
Contributor(s) Wen C, Zhao S, Yang Y
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Submission date Jan 27, 2024
Last update date May 31, 2024
Contact name Can xin Wen
E-mail(s) wcx12362379@outlook.com
Organization name Shandong University
Department Center for Reproductive Medicine
Street address 44 West Wenhua Rd
City Jinan
ZIP/Postal code 250012
Country China
 
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (9)
GSM8039440 Mcm8_WT_MEF_S9.6
GSM8039441 Mcm8_KO_MEF_S9.6
GSM8039442 MEF_No_antibody
Relations
BioProject PRJNA1070001

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE254352_RAW.tar 2.6 Gb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA

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