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Sample GSM2538379 Query DataSets for GSM2538379
Status Public on Jul 09, 2017
Title gm12878_dmso_replicate3
Sample type SRA
 
Source name gm12878_dmso
Organisms Homo sapiens; human gammaherpesvirus 4
Characteristics cell type: GM12878 [EBV+ B cell]
treated with: DMSO (vehicle)
Biomaterial provider https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC
Treatment protocol For drug treatment, we added acyclovir (Sigma-Aldrich) to 200 µM from a 100X stock solution in DMSO. Acyclovir- and vehicle-treated cells were cultured in parallel and treatment replenished with every addition of new media for at least one week.
Extracted molecule total RNA
Extraction protocol We isolated RNA from 4 × 10^6 log phase cells homogenized with a QIAshredder spin column (Qiagen). Total RNA was purified by silica-based membrane affinity as packaged in the RNeasy Mini Kit (Qiagen). Preparations included the optional DNAse treatment step. Single primer isothermal linear amplification to cDNA was achieved using the Ovation RNA-Seq System V2 (NuGEN) and 20 ng of RNA. 3 μg of cDNA was then sheared in a 40 μL volume using a Covaris S2 Focused-ultrasonicator.
We prepared deep sequencing libraries by adaptor-mediated amplification as packaged in either the Encore NGS Library System I (NuGEN) or Ovation Ultralow Library System V2 (NuGEN).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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.
Nucleotide read counts for each lytic transcript were normalized to the total number of mapped reads and integrated only over exons spanning regions that did not overlap with another transcript based on version 6 of a published B95-8 annotation.
RNA-seq profiling for every condition was performed with three biological replicates and yielded ∼60–100 million mapped sequences each experiment with reproducible transcriptome profiles.
Genome_build: hg19
Supplementary_files_format_and_content: wig files
 
Submission date Mar 16, 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 GPL23185
Series (1)
GSE96689 RNA-seq detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation.
Relations
BioSample SAMN06606758
SRA SRX2645964

Supplementary file Size Download File type/resource
GSM2538379_gm12878_dmso_replicate3.wig.gz 1021.5 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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