|
| Status |
Public on Aug 28, 2012 |
| Title |
MutuI MNase-seq Rep2 |
| 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 |
SRX174592 |
| BioSample |
SAMN01109002 |
