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Sample GSM7679499 Query DataSets for GSM7679499
Status Public on Oct 11, 2023
Title Mutu1 HiC
Sample type SRA
 
Source name Mutu1
Organism human gammaherpesvirus 4
Characteristics treatment: none
cell line: Mutu1
cell type: EBV-related Burkitt lymphoma
Treatment protocol Treatment with PARP inhibitor Olaparib was given 72 h before collection at a concentration of 5 µM. 5 million cells per condition were collected for in-situ Hi-C as per Rao et al. Cell 2014.
Growth protocol YCCEL1 and SNU719 cell lines were cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 10% and supplemented with 1% penicillin-streptomycin in a humidified incubator containing 5% CO2 at 37 ̊C
Extracted molecule genomic DNA
Extraction protocol Libraries of total ligation products were produced using Ultralow Library Systems V2 as per manufacturer’s protocol.
Purified libraries were then enriched for only EBV genome ligation products using myBaits enrichment kit as per manufacturer’s protocol.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description M.D.1.n
Data processing Illumina HiSeq 2500 paired-end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605.1) using HiC-Pro v2.10.0 pipeline
DESeq2 was used to estimate significance of differential contact based on raw count matrix files.
Only significantly changed associations (FDR<5%) were kept
Interactions were plotted as circos graph using the circlize package (version 0.4.12) of R (version 4.0.5)
Assembly: NC_007605.1
Supplementary files format and content: Raw counts for each interactions
Supplementary files format and content: p- and q-value of interactions are provided in the matrix file
 
Submission date Aug 03, 2023
Last update date Oct 11, 2023
Contact name Italo Tempera
E-mail(s) itempera@wistar.org
Organization name The Wistar Institute
Street address 3601 Spruce Street
City Philadelphia
ZIP/Postal code 10194
Country USA
 
Platform ID GPL25190
Series (2)
GSE239989 The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [HiC]
GSE239995 The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC
Relations
BioSample SAMN36826382
SRA SRX21237130

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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