|
Status |
Public on Aug 28, 2012 |
Title |
MutuI MNase-seq Rep1 |
Sample type |
SRA |
|
|
Source name |
MutuI
|
Organism |
human gammaherpesvirus 4 |
Characteristics |
assay reagents: MNase [New England Biolabs, lot#0451204, catalog#R0525M] 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 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 |
SRX174591 |
BioSample |
SAMN01109001 |