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Sample GSM2229459 Query DataSets for GSM2229459
Status Public on Jun 30, 2017
Title A_TotalDNA-seq_AkataZta+Dox+JQ1_Replicate1
Sample type SRA
Source name Akata-Zta (EBV+ Burkitt lymphoma cell line)
Organisms Homo sapiens; human gammaherpesvirus 4
Characteristics cell line: Akata-Zta
pathogen: Epstein-Barr virus
1h pretreatment: JQ1
1 day treatment: doxycycline
Treatment protocol Log phase cultures were pretreated for 1 hour with 1 μM JQ1 (EMD Millipore), I-BET/GSK525762A (EMD Millipore), RVX-208 (Cayman Chemical), or vehicle, then treated for 1 day with 500 ng/mL doxycycline (Sigma-Aldrich) or vehicle
Growth protocol Akata-Zta cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 in 5% CO2 with 10% (v/v) Tet System Approved fetal bovine serum (Clontech)
Extracted molecule genomic DNA
Extraction protocol EBV genome abundance was determined by deep sequencing of total DNA. Input chromatin was prepared as described in the paper.
Total DNA-seq libraries were prepared as described in the paper
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
Data processing Library strategy: DNA-seq
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 two mismatches and only considered reads that mapped to a unique sequence.
The percentage of EBV reads was calculated as a proportion of all reads that mapped
EBV genome abundance upon lytic induction and/or drug pretreatment was normalized to the vehicle control in each individual set of experiments
Genome_build: index contains both the human hg19 and EBV reference [GenBank ID: NC_007605.1] genomes
Supplementary_files_format_and_content: Spreadsheet shows total reads, EBV reads, and EBV quantitation
Submission date Jul 10, 2016
Last update date May 15, 2019
Contact name JJ Miranda
Organization name Barnard College, Columbia University
Street address 3009 Broadway
City New York
ZIP/Postal code 10027
Country USA
Platform ID GPL22132
Series (2)
GSE84212 BET inhibitors suppress lytic DNA replication [Akata-Zta DNA-seq]
GSE84214 BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
BioSample SAMN05370838
SRA SRX1923352

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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