{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Yihang Shen"],"instrument_platform":["NextSeq 500"],"study_type":["Capture-C"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16604"],"description":["An MNase-based proximity ligation assay analogous to a targeted Micro-4C approach was performed to study the DNA looping at CRMP4 promoter in colorectal cancer. Total four p53 binding sites (PBR1, PBR2, PBR3, PBR4) at CRMP4 promoter were investigated in each group. Total eleven groups (NC, PBR1 deletion by CRISPR-Cas9, PBR2 deletion, PBR3 deletion, PBR4 deletion, p53 knockdown, HIF1a knockdown, p53 TET domain deletion, p53 TET domain deletion plus wild type p53 overexpression in HCT116 cells in default, p53 knockdown in RKO cells, p53 knockdown in HCT8 cells) were enrolled in this study."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Circularized DNA templates were subjected to PCR amplification, and amplicons corresponding to approximately 150 bp were selected for library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat. No. E7645S, NEB).","Nucleic Acid Extraction - Nuclei were isolated and subjected to 2.5 U/μL micrococcal nuclease (MNase, Cat. No. M0247S, NEB) digestion for 10 min at 37 oC, and quenched by 4 mM EGTA. Chromatin fragments end repair was performed using T4 DNA polymerase (Cat. No. M0203S, NEB) and T4 polynucleotide kinase (Cat. No. M0201S, NEB) in the presence of dNTPs and ATP. Reactions were incubated at 20 °C for 30 min, allowing fill-in of 5’overhangs, removal of 3’ overhangs, and phosphorylation of 5’ termini. End-repaired chromatin was subsequently subjected to in situ ligation using T4 DNA ligase (Cat. No. M0202S, NEB). Crosslinks were reversed by overnight incubation at 65 °C in the presence of 100 U proteinase K (Cat. No. P8107S, NEB), and DNA was purified by phenol-chloroform extraction and ethanol precipitation. Forward and reverse primers were designed within the PBR1-4 regions to amplify ligation products derived from chromatin looping events.","Sample Collection - 1x 107 cells were crosslinked with 1% formaldehyde at room temperature for 10 min, and the reaction was quenched with 125 mM glycine.","Sequencing - The resulting libraries were sequenced using paired-end sequencing with a total sequencing depth of approximately 100K reads per library."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Yihang Shen"],"additional_accession":[]},"is_claimable":false,"name":"p53-mediated DNA looping at CRMP4 promoter in colorectal cancer","description":"An MNase-based proximity ligation assay analogous to a targeted Micro-4C approach was performed to study the DNA looping at CRMP4 promoter in colorectal cancer. Total four p53 binding sites (PBR1, PBR2, PBR3, PBR4) at CRMP4 promoter were investigated in each group. Total eleven groups (NC, PBR1 deletion by CRISPR-Cas9, PBR2 deletion, PBR3 deletion, PBR4 deletion, p53 knockdown, HIF1a knockdown, p53 TET domain deletion, p53 TET domain deletion plus wild type p53 overexpression in HCT116 cells in default, p53 knockdown in RKO cells, p53 knockdown in HCT8 cells) were enrolled in this study.","dates":{"release":"2026-02-19T00:00:00Z","modification":"2026-02-19T02:02:00.567Z","creation":"2026-02-09T11:04:56.756Z"},"accession":"E-MTAB-16604","cross_references":{"ENA":["ERP188869"],"EFO":["EFO_0002944","EFO_0004170","EFO_0007691","EFO_0005518","EFO_0004184"]}}