|
| Status |
Public on May 20, 2024 |
| Title |
KSHV-Enriched 48 h Induced BCBL-1 BR1 |
| 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 |
total RNA |
| Extraction protocol |
Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol. Ribosomal RNA was depleted from total RNA using the NEB rRNA depletion kit (E6310)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760) was used to prepare stranded RNA-Seq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
All_induced_NC009333Aligned.sorted.bam.forward.bdg.gz
All_induced_NC009333Aligned.sorted.bam.reverse.bdg.gz
|
| Data processing |
Paired-end reads were quality checked using FastQC.
Adaptors were trimmed using the Trimmomatic program with the settings, ILLUMINACLIP: adapters.fa:2:30:10, LEADING:3, TRAILING:3 and MINLEN:36.
Merged the fastq files with trimmed and paired reads from all samples.
Aligned of the merged fastq file to KSHV genome (NCBI accession number NC_009333.1) using STAR version 2.7.0b with default parameters
Generation of bedgraph coverage files using bamCoverage tool by deepTools suite
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: Signal coverage files for the KSHV genome in bedgraph 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 |
GPL24676 |
| Series (2) |
| GSE250431 |
High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing [KSHV_TRIMD_Ritu_Illumina] |
| 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 |
SAMN38882183 |
| SRA |
SRX22921017 |
