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Sample GSM2092433 Query DataSets for GSM2092433
Status Public on Jul 08, 2016
Title Akata_induced
Sample type SRA
 
Source name Akata_induced
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 x 106 cells/ml in fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) plus 10 μg/ml anti-IgG.
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)
Iso-Seq
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model PacBio RS II
 
Data processing Library strategy: Iso-Seq
SMRTportal RS_IsoSeq v.1 with ICE to obtain full-length consensus isoforms
Alignment to the EBV genome (NCBI accession number KC207813.1) using GMAP 2014-07-21 with the parameter -n 1
TRIMD end validator and TRIMD start validator to produce bedgraph files of isoform 5' and 3' ends
Genome_build: KC207813.1
Supplementary_files_format_and_content: BedGraph files of isoform 5' and 3' ends
 
Submission date Mar 17, 2016
Last update date Jan 31, 2022
Contact name Erik K Flemington
E-mail(s) eflemin@tulane.edu
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 GPL21311
Series (2)
GSE79335 Global transcript structure resolution of high gene density genomes through multi-platform data integration: Iso-Seq
GSE79337 Global transcript structure resolution of high gene density genomes through multi-platform data integration
Relations
BioSample SAMN04563763
SRA SRX1639559

Supplementary file Size Download File type/resource
GSM2092433_Akata_induced_Iso-Seq_read_ends.bedgraph.gz 3.4 Kb (ftp)(http) BEDGRAPH
GSM2092433_Akata_induced_Iso-Seq_read_starts.bedgraph.gz 15.2 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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