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Sample GSM2091149 Query DataSets for GSM2091149
Status Public on Jul 08, 2016
Title Induced negative control GapmeR 1
Sample type SRA
Source name Induced negative control GapmeR 1
Organism Homo sapiens
Characteristics cell type: Akata cells
Treatment protocol One day prior to induction, near-saturation cell cultures were diluted with equal volumes of fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep). The next day, cells were spun down and resuspended at a concentration of 1×106 cells/ml in fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) plus either 10 μg/ml anti-IgG or no anti-IgG (uninduced). For GapmeR treatment, 3 × 106 cells in RPMI (with 10% FBS) were nucleofected (Lonza) with 600 pmol of either negative control GapmeR A or targeted GapmeR. On the following day an equal volume of RPMI (with 10% FBS) was added with either 20 μg/ml anti-IgG or no anti-IgG (uninduced).
Growth protocol Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in RPMI 1640 plus 10% fetal bovine serum and 0.5% Penicillin-Streptomycin.
Extracted molecule polyA RNA
Extraction protocol TRIzol reagent (Ambion) followed byb DNase (Ambion) treatment
Illumina TruSeq Stranded protocol
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Illumina 1.9 basecalling
Alignment to the Akata EBV genome (NCBI accession number KC207813.1) using STAR version with default parameters
Generation of signalmap files using IGVTools
Genome_build: KC207813.1
Supplementary_files_format_and_content: Signalmap coverage files for the Akata genome
Submission date Mar 16, 2016
Last update date Jan 31, 2022
Contact name Erik K Flemington
Phone 504 988-1167
Organization name Tulane Health Sciences Center
Department Pathology
Street address 1430 Tulane Ave., SL79
City New Orleans
State/province LA
ZIP/Postal code 70112
Country USA
Platform ID GPL11154
Series (2)
GSE79304 Global transcript structure resolution of high gene density genomes through multi-platform data integration: Illumina RNA-Seq
GSE79337 Global transcript structure resolution of high gene density genomes through multi-platform data integration
BioSample SAMN04563776
SRA SRX1639572

Supplementary file Size Download File type/resource
GSM2091149_Akata_induced_EBV_ncgapA_rep1_minus.wig.gz 544.7 Kb (ftp)(http) WIG
GSM2091149_Akata_induced_EBV_ncgapA_rep1_plus.wig.gz 510.5 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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