|
| Status |
Public on May 20, 2024 |
| Title |
Uninduced iSLK-WTBAC |
| Sample type |
SRA |
| |
|
| Source name |
iSLK
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iSLK
cell type: Endothelial Cells
genotype: WT
treatment: Uninduced
|
| Treatment protocol |
Induction with Doxorubicin (1 ug/ml) and sodium butyrate (1 mM).
|
| Growth protocol |
Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in DMEM plus 10% fetal bovine serum, 1% Penicillin-Streptomycin, 1 μg/ml puromycin, 250 μg/ml G418 and 250 μg/ml hygromycin
|
| 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). PCR-cDNA sequencing libraries were prepared by using SQK-PCB109 (ONT) library preparation kit with 1 ng of each polyA-selected RNA sample.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Data processing |
Merged the fastq files that were assigned "passed.fastq".
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 in both default and flipped (anti-sense) orientations
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: Transcript structures in gtf format
Library strategy: PCR-cDNA Sequencing
|
| |
|
| Submission date |
Dec 18, 2023 |
| Last update date |
May 20, 2024 |
| Contact name |
Rolf Renne |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Florida
|
| Street address |
1200 Newell Dr.
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (2) |
| GSE250434 |
High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing [iSLK-WTBAC-PCR-cDNA-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 |
SAMN38882047 |
| SRA |
SRX22920301 |
