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Sample GSM982656 Query DataSets for GSM982656
Status Public on Aug 28, 2012
Title Raji EBNA1 ChIP
Sample type SRA
Source name Raji
Organism human gammaherpesvirus 4
Characteristics assay reagents: EBNA1 antibody [a custom polyclonal antibody made for us by the Pocono Rabbit Farm and Laboratory Inc, clone# 25139]
ebv-positive, human cell line: Raji
Treatment protocol Nuclei were isolated from 50M Mutu and Mutu-LCL cells with a Dounce homogenizer and treated with MNase (500 U/ml).
Growth protocol RPMI1640 5% CO2
Extracted molecule genomic DNA
Extraction protocol Micrococcal nuclease I (MNase I) resistant DNA was extracted by phenol-chloroform and ethanol precipitation. The 150 bp mononucleosomal DNA was isolated from 1.5% agarose gel and purified by the QIAquick Gel extraction kit (QIAGEN) according to the manufacturer's protocol.
ChIP-Seq experiments were performed with 2 × 106 Raji cells per IP with either EBNA1 monoclonal antibody or control mouse IgG. Quantification of precipitated DNA was determined using real-time PCR and the standard curve method for absolute quantitation (ABI 7000 Real-Time PCR System).
For both experiments, purified DNA was then subject to sequencing according to the manufacturer's recommendations (Illumina).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Raji EBNA1 ChIP
Data processing Base calling was performed using Illumina software pipeline (Genome Analyzer)
Align to the human genome (hg19 UCSC) using bowtie (version 0.12.7) allowing 1 mismatch and reporting only uniquely aligning hits. Unmapped hits were saved into a separate file and reads with more than one alignment in the human genome were discarded (--max /dev/null)
Align to the EBV genome (NC_007605) was performed on the unmapped reads that had no hits in the human genome. Bowtie version and parameters as human genome.
Peak calling was perfomed on the viral genome using a cutoff of 30 reads per million
Genome_build: Viral genome: March 2010 NC_007605
Supplementary_files_format_and_content: Bowtie-generated WIG files
Submission date Aug 08, 2012
Last update date May 15, 2019
Contact name Aaron Arvey
Organization name Memorial Sloan-Kettering Cancer Center
Street address 415 E 68th St ZRC 1441
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platform ID GPL15906
Series (1)
GSE39913 EBNA1 ChIP-seq and MNase-seq in EBV-positive MUTU cell lines
SRA SRX174589
BioSample SAMN01108999

Supplementary file Size Download File type/resource
GSM982656_s_2_sequence_EBNA.hg19.bowtie.unmapped.ebv.bowtie.align.vals.wig.gz 466.5 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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