|
| Status |
Public on Nov 13, 2017 |
| Title |
ATZ LGNFR+ DNA seq rep 5 |
| Sample type |
SRA |
| |
|
| Source name |
ATZ LGNFR+ DNA-seq
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
cell type: EBV-positive Akata-Zta cells
pretreated with: 200 μM acyclovir for 1 hour
sorted fraction: LGNFR+
|
| Treatment protocol |
Akata-Zta cells were pretreated with 200 μM acyclovir for 1 hour before reactivation of the lytic cycle with 500 ng/mL doxycycline. After 1 day, cells were magnetically sorted using LNGFR Microbeads and LS columns (Miltenyi Biotech).
|
| Growth protocol |
EBV-positive Akata-Zta cells (Ramasubramanyan et al., 2015) 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).
|
| 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 |
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to two mismatches 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 03, 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) |
| GSE98123 |
The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation |
| GSE98498 |
The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [DNA-seq] |
|
| Relations |
| BioSample |
SAMN06885944 |
| SRA |
SRX2780406 |
