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Sample GSM5431866 Query DataSets for GSM5431866
Status Public on Sep 23, 2021
Title HiChIP: uninfected Ramos B cells replicate 1
Sample type SRA
 
Source name Uninfected Ramos B cells
Organism Homo sapiens
Characteristics cell line: Ramos B cells
infection: None
chip antibody: anti-H3K27ac antibody (Abcam ab4729)
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) (http://aryeelab.org/hichipper) 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) (http://aryeelab.org/hichipper) 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 hicpro2juicebox.sh script from HiC-Pro (Servant et al. 2015) and KR normalized using Juicer Tools (https://github.com/aidenlab/juicer/wiki/Juicer-Tools-Quick-Start)
 
Submission date Jul 08, 2021
Last update date Oct 23, 2023
Contact name Matthew Weirauch
E-mail(s) Matthew.Weirauch@cchmc.org
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]
Relations
BioSample SAMN20124832
SRA SRX11385198

Supplementary file Size Download File type/resource
GSM5431866_HiChIP_uninfected_rep1.hg19.allValidPairs.txt.gz 479.7 Mb (ftp)(http) TXT
GSM5431866_HiChIP_uninfected_rep1.hg19.hic 1.4 Gb (ftp)(http) HIC
GSM5431866_HiChIP_uninfected_rep1.hg19.mango.txt.gz 1.1 Mb (ftp)(http) TXT
GSM5431866_HiChIP_uninfected_rep1.hg38.allValidPairs.txt.gz 453.6 Mb (ftp)(http) TXT
GSM5431866_HiChIP_uninfected_rep1.hg38.hic 1.4 Gb (ftp)(http) HIC
GSM5431866_HiChIP_uninfected_rep1.hg38.mango.txt.gz 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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