GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
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
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jan 27, 2024
Last update date May 31, 2024
Contact name Can xin Wen
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
BioProject PRJNA1070001

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap