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Sample GSM7979080 Query DataSets for GSM7979080
Status Public on May 20, 2024
Title 24h Induced BCBL-1
Sample type SRA
 
Source name BCBL-1
Organism Homo sapiens
Characteristics cell line: BCBL-1
cell type: Primary effusion lymphoma cells
genotype: WT
treatment: Induced
Treatment protocol Induction with 12-O-tetradecanoylphorbol-13-acetate (TPA) (20 ng/ml) and sodium butyrate (2 mM) for 48 h
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 1% Penicillin-Streptomycin.
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol.
Poly(A)-tailed RNA was selected from 75 μg of each RNA sample using Dyna Beads mRNA purification kit (Invitrogen, Catalog No. 61006). Direct-RNA sequencing libraries were prepared by using SQK-RNA002 (ONT) library preparation kit with 50 ng of each polyA-selected RNA sample.
direct-RNA Sequencing
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model MinION
 
Data processing Merged the fastq files that were assigned "passed.fastq" by the minKnow software.
Aligned of the fastq file to KSHV genome (NCBI accession number NC_009333.1) using minimap2
Generated gtf files from KSHV aligned bam files to identify transcript structures
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: Transcript structures in gtf format
 
Submission date Dec 18, 2023
Last update date May 20, 2024
Contact name Rolf Renne
E-mail(s) rrenne@ufl.edu
Organization name University of Florida
Street address 1200 Newell Dr.
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
 
Platform ID GPL24106
Series (2)
GSE250429 High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing [BCBL-1-directRNA-Seq]
GSE250435 High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing
Relations
BioSample SAMN38882173
SRA SRX22920597

Supplementary file Size Download File type/resource
GSM7979080_BCBL-1-24h-Induced-directRNA.gtf.gz 1.8 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA

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