|
| Status |
Public on Sep 23, 2021 |
| Title |
HiChIP: EBNA2- (P3HR1) EBV infected Ramos B cells replicate 2 |
| 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) (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)
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| |
|
| 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 |
SAMN20124827 |
| SRA |
SRX11385203 |
