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Sample GSM2091013 Query DataSets for GSM2091013
Status Public on Jul 08, 2016
Title Akata_induced_rep1_DNase
Sample type SRA
Source name Akata_induced_rep1_DNase
Organism Homo sapiens
Characteristics cell type: Akata cells
treatmemt: DNAse
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).
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 total RNA
Extraction protocol TRIzol (Ambion). A portion of each replicate was treated with DNAse (Ambion) and a portion left untreated for a total of 4 samples.
Library strategy RNA-Seq
Library source transcriptomic
Library selection CAGE
Instrument model Illumina HiSeq 2500
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 with IGVTools, using reads with primary alignments
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 GPL16791
Series (2)
GSE79293 Global transcript structure resolution of high gene density genomes through multi-platform data integration: deepCAGE
GSE79337 Global transcript structure resolution of high gene density genomes through multi-platform data integration
BioSample SAMN04564259
SRA SRX1639579

Supplementary file Size Download File type/resource
GSM2091013_Akata_induced_rep1_DNAse_EBV_minus.wig.gz 220.1 Kb (ftp)(http) WIG
GSM2091013_Akata_induced_rep1_DNAse_EBV_plus.wig.gz 207.5 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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