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Sample GSM982660 Query DataSets for GSM982660
Status Public on Aug 28, 2012
Title MutuI Input Control (Matched to MNase-seq) Rep1
Sample type SRA
 
Source name MutuI
Organism human gammaherpesvirus 4
Characteristics assay reagents: NA
ebv-positive, human cell line: Mutu
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 MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina Genome Analyzer
 
Description MutuI IgG Control (Matched to MNase-seq)
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
E-mail(s) aarvey@cbio.mskcc.org
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
Relations
SRA SRX174593
BioSample SAMN01109003

Supplementary file Size Download File type/resource
GSM982660_s_7_sequence.hg19.bowtie.unmapped.ebv.bowtie.align.vals.wig.gz 444.9 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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