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Sample GSM2229488 Query DataSets for GSM2229488
Status Public on Jun 30, 2017
Title ChIP-seq_H3K27ac_Mutu_Replicate1
Sample type SRA
 
Source name MutuI (EBV+ Burkitt lymphoma cell line)
Organisms Homo sapiens; human gammaherpesvirus 4
Characteristics cell line: MutuI
pathogen: Epstein-Barr virus
chip antibody: H3K27ac
Treatment protocol Cells were not treated
Growth protocol MutuI cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 in 5% CO2 with 10% (v/v) fetal bovine serum (Invitrogen)
Extracted molecule genomic DNA
Extraction protocol DNA was prepared and ChIP performed as described in the paper
ChIP-seq libraries were prepared as described in the paper
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing 50 bp reads were mapped using Bowtie to an index containing both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes.
Parameters allowed for up to 2 mismatches and 2 alignments
Peaks were visualized after normalization to the background baseline
Formatted for uploading to Integrative Genomics Viewer (www.broadinstitute.org/igv/)
Genome_build: index contains both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes
Supplementary_files_format_and_content: Wigs are formatted for IGV. Genome file chrEBV(B95_8_Raji).fa is available from http://www.flemingtonlab.com/rnaseq.html. Wig columns are chromosome, start, stop, counts per million mapped reads.
 
Submission date Jul 10, 2016
Last update date May 15, 2019
Contact name JJ Miranda
E-mail(s) jmiranda@barnard.edu
Organization name Barnard College, Columbia University
Street address 3009 Broadway
City New York
ZIP/Postal code 10027
Country USA
 
Platform ID GPL22131
Series (2)
GSE84213 BET proteins bind the lytic origins of replication [MutuI ChIP-seq]
GSE84214 BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
Relations
BioSample SAMN05370823
SRA SRX1923326

Supplementary file Size Download File type/resource
GSM2229488_sml18_m2.maphv.grep.xy.mask.norm.igv.wig.gz 1.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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