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Sample GSM2597436 Query DataSets for GSM2597436
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
 
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 SAMN06885948
SRA SRX2780402

Supplementary file Size Download File type/resource
GSM2597436_ATZ_Lp_DNAseq_rep3.igv.wig.gz 917.9 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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