|
Status |
Public on Nov 13, 2017 |
Title |
ATZ LGNFR- DNA seq rep 3 |
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
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|
|
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 |
SAMN06885947 |
SRA |
SRX2780403 |