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Sample GSM5431871 Query DataSets for GSM5431871
Status Public on Sep 23, 2021
Title HiChIP: EBNA2- (P3HR1) EBV infected Ramos B cells replicate 1
Sample type SRA
Source name EBNA2- (P3HR1) EBV infected Ramos B cells
Organism Homo sapiens
Characteristics cell line: Ramos B cells
infection: EBNA- (P3HR1) Epstein-Barr virus (EBV)
chip antibody: anti-H3K27ac antibody (Abcam ab4729)
Treatment protocol Ramos B cells were infected with EBNA- (P3HR1) Epstein-Barr virus (EBV).
Growth protocol Cells were cultured in 10% FBS supplemented RPMI medium 1640 for 2 weeks.
Extracted molecule genomic DNA
Extraction protocol HiChIP-seq libraries were prepared following Mumbach et al. (Mumbach et al. 2016).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Library strategy: HiChIP
Pooled samples were created by combining the fastq files for replicates 1 and 2. Analyses were performed on the pooled samples only.
We used HiC-Pro (version: 2.11.0) to identify Hi-C contact maps (Servant et al. 2015).
We then used hichipper (version: 0.7.3) ( to correct the background, perform restriction site bias modeling and obtain looping information.
We identified differential looping events using the diffloop Bioconductor R package (1.6.0) (Lareau and Aryee 2018). Briefly, to calculate EBNA2-dependent differential looping, we first determined EBV-dependent chromatin looping by comparing EBVEBNA2+ looping events to uninfected looping events using diffloop (>1.5 fold, p-value < 0.05).
Genome_build: hg19
Genome_build: hg38
Supplementary_files_format_and_content: allValidPair files were created with HiC-Pro and contain 12 columns: 1) read name; 2) read 1 chromosome; 3) read 1 position; 4) read 1 strand; 5) read 2 chromosome; 6) read 2 position; 7) read 2 strand; 8) fragment size; 9) read 1 restriction fragment name; 10) read 2 restriction fragment name; 11) read 1 mapping quality; 12) read 2 mapping quality
Supplementary_files_format_and_content: mango.txt files (containing intrachromosomal loops) were generated using hichipper (version: 0.7.3) ( and contain 8 columns: 1) fragment 1 chromosome; 2) fragment 1 start; 3) fragment 1 end; 4) fragment 2 chromosome; 5) fragment 2 start; 6) fragment 2 end; 7) number of paired end tags supporting the interaction; 8) adjusted p-value
Supplementary_files_format_and_content: hic files (visualization files) were generated using the script from HiC-Pro (Servant et al. 2015) and KR normalized using Juicer Tools (
Submission date Jul 08, 2021
Last update date Oct 23, 2023
Contact name Matthew Weirauch
Organization name Cincinnati Children's Hospital Medical Center
Department Center for Autoimmune Genomics and Etiology (CAGE)
Street address 3333 Burnet Avenue
City Cincinnati
State/province Ohio
ZIP/Postal code 45229-3026
Country USA
Platform ID GPL18573
Series (2)
GSE148396 Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci
GSE179755 Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci [HiChIP]
BioSample SAMN20124828
SRA SRX11385202

Supplementary file Size Download File type/resource
GSM5431871_HiChIP_P3HR1_rep1.hg19.allValidPairs.txt.gz 483.6 Mb (ftp)(http) TXT
GSM5431871_HiChIP_P3HR1_rep1.hg19.hic 1.4 Gb (ftp)(http) HIC 1.1 Mb (ftp)(http) TXT
GSM5431871_HiChIP_P3HR1_rep1.hg38.allValidPairs.txt.gz 457.5 Mb (ftp)(http) TXT
GSM5431871_HiChIP_P3HR1_rep1.hg38.hic 1.4 Gb (ftp)(http) HIC 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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