|
| Status |
Public on Jun 30, 2017 |
| Title |
A_TotalDNA-seq_AkataZta+Dox+JQ1_Replicate2 |
| 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 |
| 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 |
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 |
|
| Relations |
| BioSample |
SAMN05370839 |
| SRA |
SRX1923353 |
