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Sample GSM2229423 Query DataSets for GSM2229423
Status Public on Jun 30, 2017
Title TotalDNA-seq_MutuI+JQ1_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
1h pretreatment: JQ1
1 day treatment: vehicle
Treatment protocol Log phase cultures were pretreated for 1 hour with 1 μM JQ1 (EMD Millipore) or vehicle, then treated for 1 day with 10 μg/mL goat anti-human IgG, IgM, IgA secondary antibody (Thermo Scientific, PI31128) or vehicle
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 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 2500
 
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
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)
GSE84210 BET inhibitors suppress BZLF1 expression [MutuI DNA-seq]
GSE84214 BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
Relations
BioSample SAMN05370881
SRA SRX1923394

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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