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Sample GSM2611579 Query DataSets for GSM2611579
Status Public on Jun 30, 2017
Title ChIP-seq_BRD4_AkataZta_acy_vehicle_LGNFR-_Replicate2
Sample type SRA
 
Source name Akata-Zta cells
Organisms Homo sapiens; human gammaherpesvirus 4
Characteristics cell line: Akata-ZTA
pathogen: Epstein-Barr virus
chip antibody: BRD4
Treatment protocol Log-phase cultures were pretreated with 1) 200 μM acyclovir (Sigma-Aldrich) and 2) either 1 uM JQ1 or vehicle (DMSO) for 1 hr before induction with 500 ng/mL doxycycline (Sigma-Aldrich). After 1 day, cells were magnetically sorted using LNGFR Microbeads and LS columns (Miltenyi Biotec).
Growth protocol Cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) Tet System Approved fetal bovine serum (Clontech) in 5% CO2 at 37°C.
Extracted molecule genomic DNA
Extraction protocol 18E6 cells were collected, and ChIP was performed as described in the paper.
Deep sequencing libraries were prepared by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing 50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to 2 mismatches and 2 alignments
The number of hits at each base was counted and then normalized per million mapped reads.
Formatted for uploading to the Integrative Genomics Viewer (www.broadinstitute.org/igv)
Genome_build: hg19, EBV NC_007605.1
Supplementary_files_format_and_content: wig files
 
Submission date May 10, 2017
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 GPL23362
Series (2)
GSE84214 BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
GSE98773 JQ1 prevents BRD4 recruitment to the lytic origins of replication [Akata-Zta Brd4 ChIP-seq]
Relations
BioSample SAMN06927267
SRA SRX2795371

Supplementary file Size Download File type/resource
GSM2611579_AkataZta_acy_veh_Ln_BRD4_ChIP-seq_rep2.igv.wig.gz 972.0 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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