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Sample GSM2229435 Query DataSets for GSM2229435
Status Public on Jun 30, 2017
Title A_RNA-seq_AkataZta+JQ1_Replicate1
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: vehicle
Treatment protocol Log phase cultures were pretreated for 1 hour with 1 μM JQ1 (EMD Millipore), I-BET/GSK525762A (EMD Millipore), 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 total RNA
Extraction protocol RNA was extracted and cDNA was prepared as described in the paper
RNA-seq libraries were prepared as described in the paper
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing 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 number of hits at each base was counted and then normalized per million mapped reads.
Formatted for uploading to Integrative Genomics Viewer (www.broadinstitute.org/igv/)
Genome_build: Index contains both the human hg19 and EBV [GenBank ID: NC_007605.1] reference genomes
Supplementary_files_format_and_content: Wigs are formatted for IGV. Genome file chrEBV(B95_8_Raji).fa is available from http://www.flemingtonlab.com/rnaseq.html. Wig columns are chromosome, start, stop, counts per million mapped reads.
 
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)
GSE84211 BET inhibitors suppress lytic DNA replication [Akata-Zta RNA-seq]
GSE84214 BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
Relations
BioSample SAMN05370865
SRA SRX1923376

Supplementary file Size Download File type/resource
GSM2229435_KMK_96-m1.maphv.grep.xy.xyn.igv.wig.gz 807.9 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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