|
| Status |
Public on May 20, 2024 |
| Title |
KSHV_Enriched_BCBL-1_48h_induced_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 |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol.
Full-length cDNAs were prepared using Low Input RNA: cDNA Synthesis and Amplification kit (NEB, Catalog No. E6421) as per the manufacturer’s guidelines. Full-length cDNAs were hybridized with KSHV baits to capture the KSHV specific cDNAs for preapring KSHV-Enriched libraries. cDNAs were size-fractionated and re-amplified. SMRTbell library adapters were ligated to cDNA fractions for preparing PacBio SMRT-Seq libraries.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Sequel |
| |
|
| Description |
IsoSeq_CFLs_NC009333_mapped.read_ends.bedgraph.gz
IsoSeq_CFLs_NC009333_mapped.read_starts.bedgraph.gz
|
| Data processing |
Library strategy: IsoSeq
Circular Consensus sequences (.ccs.bam) files for all samples were processed together by the IsoSeq pipeline to generate consensus full length (CFLs) reads from all samples.
CFLs were mapped to the KSHV reference genome (NCBI accession number NC_009333.1) using gmap tool for long read sequence alignment.
TRIMD end validator and TRIMD start validator scripts were run to produce bedgraph files of isoform 5' and 3' ends
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: BedGraph files of isoform 5' and 3' ends
Library strategy: Iso-Seq
|
| |
|
| 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 |
GPL26180 |
| Series (2) |
| GSE250432 |
High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing [Iso-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 |
SAMN38882193 |
| SRA |
SRX22920695 |
