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Series GSE250219 Query DataSets for GSE250219
Status Public on Aug 12, 2024
Title Direct mapping of G-quadruplex anchored 3D chromatin structure via ViCAR
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary We developed ViCAR (viewpoint HiCAR), a technique that uses antibody-based capture of genome features and their interacting chromatin domains. ViCAR uncovers numerous cell-type-specific G4-dependent enhancer-promoter interactions and is easily extended to other features such as histone marks. ViCAR represents a practical and powerful tool to explore the relationship between epigenetic marks and 3D genome interactomes.
 
Overall design ViCAR to capture genome architecture associated with G4s and histone marks in K562 and hESCs.
 
Contributor(s) Flynn SM, Dhir S, Balasubramanian S
Citation(s) 39227991
Submission date Dec 14, 2023
Last update date Sep 30, 2024
Contact name Somdutta Dhir
E-mail(s) sd997@cam.ac.uk
Organization name University of Cambridge
Department CRUK-CI
Lab Balasubramanian
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL30172 NextSeq 2000 (Mus musculus)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (79)
GSM7975753 K562_BG4_ViCAR_rep1
GSM7975754 K562_BG4_ViCAR_rep1_reseq
GSM7975755 K562_BG4_ViCAR_rep1_reseq2
Relations
BioProject PRJNA1052689

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
GSE250219_G4_mutant_RNAseq.xlsx 1.8 Mb (ftp)(http) XLSX
GSE250219_G4_mutant_clone1_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05.bed.gz 1.0 Mb (ftp)(http) BED
GSE250219_G4_mutant_clone1_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05_WashU.bed.gz 192.8 Kb (ftp)(http) BED
GSE250219_G4_mutant_clone1_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 75.9 Kb (ftp)(http) TBI
GSE250219_G4_mutant_clone1_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05.bed.gz 218.5 Kb (ftp)(http) BED
GSE250219_G4_mutant_clone1_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 42.1 Kb (ftp)(http) BED
GSE250219_G4_mutant_clone1_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 22.1 Kb (ftp)(http) TBI
GSE250219_G4_mutant_clone2_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05.bed.gz 1022.3 Kb (ftp)(http) BED
GSE250219_G4_mutant_clone2_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05_WashU.bed.gz 186.9 Kb (ftp)(http) BED
GSE250219_G4_mutant_clone2_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 73.5 Kb (ftp)(http) TBI
GSE250219_G4_mutant_clone2_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05.bed.gz 227.6 Kb (ftp)(http) BED
GSE250219_G4_mutant_clone2_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 44.5 Kb (ftp)(http) BED
GSE250219_G4_mutant_clone2_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 23.2 Kb (ftp)(http) TBI
GSE250219_GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05.bed.gz 910.3 Kb (ftp)(http) BED
GSE250219_GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05_WashU.bed.gz 168.8 Kb (ftp)(http) BED
GSE250219_GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 60.7 Kb (ftp)(http) TBI
GSE250219_H1_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05.bed.gz 710.7 Kb (ftp)(http) BED
GSE250219_H1_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 137.1 Kb (ftp)(http) BED
GSE250219_H1_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 60.3 Kb (ftp)(http) TBI
GSE250219_H1_H3K27me3_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05.bed.gz 10.8 Mb (ftp)(http) BED
GSE250219_H1_H3K27me3_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 1.7 Mb (ftp)(http) BED
GSE250219_H1_H3K27me3_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 194.4 Kb (ftp)(http) TBI
GSE250219_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05.bed.gz 1.9 Mb (ftp)(http) BED
GSE250219_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 340.0 Kb (ftp)(http) BED
GSE250219_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 101.7 Kb (ftp)(http) TBI
GSE250219_K562_G4_mutant_clone1_Pol2_5SP_CnT_rep1.markduplicates.s600.cpm.bs3.bw 231.6 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone1_Pol2_5SP_CnT_rep2.markduplicates.s600.cpm.bs3.bw 201.3 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone1_Pol2_5SP_CnT_rep3.markduplicates.s600.cpm.bs3.bw 318.8 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone1_Pol2_5SP_CnT_rep4.markduplicates.s600.cpm.bs3.bw 255.3 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone1_Pol2_5SP_CnT_rep5.markduplicates.s600.cpm.bs3.bw 332.3 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone1_Pol2_5SP_CnT_rep6.markduplicates.s600.cpm.bs3.bw 305.2 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone1_Pol2_5SP_CnT_rep7.markduplicates.s600.cpm.bs3.bw 306.3 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone2_Pol2_5SP_CnT_rep1.markduplicates.s600.cpm.bs3.bw 191.4 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone2_Pol2_5SP_CnT_rep2.markduplicates.s600.cpm.bs3.bw 182.4 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone2_Pol2_5SP_CnT_rep3.markduplicates.s600.cpm.bs3.bw 334.2 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone2_Pol2_5SP_CnT_rep4.markduplicates.s600.cpm.bs3.bw 273.8 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone2_Pol2_5SP_CnT_rep5.merged.markduplicates.s600.cpm.bs3.bw 289.4 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone2_Pol2_5SP_CnT_rep6.markduplicates.s600.cpm.bs3.bw 262.9 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone2_Pol2_5SP_CnT_rep7.markduplicates.s600.cpm.bs3.bw 175.3 Mb (ftp)(http) BW
GSE250219_K562_G4_mutant_clone_1_.10_01kb.interactions_FitHiC_Q0.01.bed.gz 10.3 Mb (ftp)(http) BED
GSE250219_K562_G4_mutant_clone_1_.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz 1.7 Mb (ftp)(http) BED
GSE250219_K562_G4_mutant_clone_1_.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz.tbi.gz 323.0 Kb (ftp)(http) TBI
GSE250219_K562_G4_mutant_clone_2_.10_01kb.interactions_FitHiC_Q0.01.bed.gz 13.0 Mb (ftp)(http) BED
GSE250219_K562_G4_mutant_clone_2_.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz 2.1 Mb (ftp)(http) BED
GSE250219_K562_G4_mutant_clone_2_.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz.tbi.gz 363.9 Kb (ftp)(http) TBI
GSE250219_K562_H3K4me1_ViCAR_FitHiC_Q0.05.bed.gz 19.3 Mb (ftp)(http) BED
GSE250219_K562_H3K4me1_ViCAR_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 326.3 Kb (ftp)(http) TBI
GSE250219_K562_H3K4me1_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 3.1 Mb (ftp)(http) BED
GSE250219_K562_H3K4me3_ViCAR_rep1_prefix.5kb.interactions_FitHiC_Q0.05.bed.gz 19.6 Mb (ftp)(http) BED
GSE250219_K562_H3K4me3_ViCAR_rep1_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 3.1 Mb (ftp)(http) BED
GSE250219_K562_H3K4me3_ViCAR_rep1_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 403.1 Kb (ftp)(http) TBI
GSE250219_K562_H3K4me3_ViCAR_rep2_prefix.5kb.interactions_FitHiC_Q0.05.bed.gz 18.3 Mb (ftp)(http) BED
GSE250219_K562_H3K4me3_ViCAR_rep2_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 2.9 Mb (ftp)(http) BED
GSE250219_K562_H3K4me3_ViCAR_rep2_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 396.2 Kb (ftp)(http) TBI
GSE250219_K562_WT_HiCAR.10_01kb.interactions_FitHiC_Q0.01.bed.gz 12.3 Mb (ftp)(http) BED
GSE250219_K562_WT_HiCAR.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz 2.0 Mb (ftp)(http) BED
GSE250219_K562_WT_HiCAR.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz.tbi.gz 342.1 Kb (ftp)(http) TBI
GSE250219_K562_WT_Pol2_5SP_CnT_rep1.markduplicates.s600.cpm.bs3.bw 229.5 Mb (ftp)(http) BW
GSE250219_K562_WT_Pol2_5SP_CnT_rep2.markduplicates.s600.cpm.bs3.bw 197.2 Mb (ftp)(http) BW
GSE250219_K562_WT_Pol2_5SP_CnT_rep3.markduplicates.s600.cpm.bs3.bw 335.6 Mb (ftp)(http) BW
GSE250219_K562_WT_Pol2_5SP_CnT_rep4.markduplicates.s600.cpm.bs3.bw 233.1 Mb (ftp)(http) BW
GSE250219_K562_WT_Pol2_5SP_CnT_rep5.markduplicates.s600.cpm.bs3.bw 239.5 Mb (ftp)(http) BW
GSE250219_K562_WT_Pol2_5SP_CnT_rep6.markduplicates.s600.cpm.bs3.bw 321.2 Mb (ftp)(http) BW
GSE250219_K562_WT_Pol2_5SP_CnT_rep7.markduplicates.s600.cpm.bs3.bw 299.8 Mb (ftp)(http) BW
GSE250219_WT_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05.bed.gz 2.7 Mb (ftp)(http) BED
GSE250219_WT_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05_WashU.bed.gz 472.5 Kb (ftp)(http) BED
GSE250219_WT_K562_BG4_ViCAR_prefix.10kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 137.5 Kb (ftp)(http) TBI
GSE250219_WT_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05.bed.gz 838.8 Kb (ftp)(http) BED
GSE250219_WT_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz 155.6 Kb (ftp)(http) BED
GSE250219_WT_K562_BG4_ViCAR_prefix.5kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi.gz 59.7 Kb (ftp)(http) TBI
GSE250219_mESC_H3K27me3_ViCAR.05_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz 1.9 Mb (ftp)(http) BED
GSE250219_mESC_H3K27me3_ViCAR.05_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz.tbi.gz 266.8 Kb (ftp)(http) TBI
GSE250219_mESC_H3K27me3_ViCAR_05_01kb.interactions_FitHiC_Q0.01.bed.gz 12.1 Mb (ftp)(http) BED
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Processed data are available on Series record
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