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Sample GSM7679534 Query DataSets for GSM7679534
Status Public on Oct 11, 2023
Title YCCEL1 H3K27ac HiChIP rep1
Sample type SRA
 
Source name YCCEL1
Organisms Homo sapiens; human gammaherpesvirus 4
Characteristics chip antibody: H3K27ac (Active Motif 39133)
cell line: YCCEL1
cell type: Gastric adenocarcinoma
infection: Human gammaherpesvirus 4
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 25 million cells were fixed with 1% formaldehyde for 10 min and then quenched with 0.125 M glycine for 5 min at RT. Ligation products were immunoprecipitated with 25 µg H3K27ac (Active Motif 39133). 5 μL of Streptavidin C-1 beads were used for biotin pull-down.
After the last wash with Tween Wash Buffer bead-bound DNA was used to prepare libraries with Ultralow Library Systems V2 (Tecan Genomics, part no. 0344NB-32) as per manufacturer’s protocol
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
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
hichipper software was used to perform restriction site bias modeling and interaction identification.
diffloop R package was used to estimate significance of differential contact based on raw count matrix files. Only significantly changed associations (FDR<1%) were kept
EBV-EBV interactions were visualized using UCSC Genome Browser, EBV-Human interactions were plotted as circos graph using the circlize package (version 0.4.12) of R (version 4.0.5)
Assembly: hg19, NC_007605.1
Supplementary files format and content: mango files listing all interactions with the respective p-value
Supplementary files format and content: bedpe files listing all interchromosomal interactions with respective read counts
Library strategy: HiChIP
 
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 GPL23185
Series (2)
GSE239992 The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [HiChIP]
GSE239995 The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC
Relations
BioSample SAMN36830731
SRA SRX21242817

Supplementary file Size Download File type/resource
GSM7679534_YCCEL1-H3K27ac-rep1.inter.loop_counts.bedpe.gz 5.0 Mb (ftp)(http) BEDPE
GSM7679534_YCCEL1-H3K27ac-rep1.interactions.all.mango.txt.gz 3.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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