|
| 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 |
