|
| Status |
Public on Jun 30, 2017 |
| Title |
TotalDNA-seq_Akata-Zta+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
|
| 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 |
DNA was isolated from 1 million cells each of LGNFR+ and LGNFR- using a Qiagen DNeasy Blood and Tissue kit.
Deep sequencing libraries were prepared by adaptor-mediated amplification using Ovation Ultralow Library System V2 (NuGEN).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: DNA-seq
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to one mismatch and only considered reads that mapped to a unique sequence.
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 |
| GSE98772 |
JQ1 prevents BRD4 recruitment to the lytic origins of replication [Akata-Zta DNA-seq] |
|
| Relations |
| BioSample |
SAMN06927276 |
| SRA |
SRX2795378 |
