|
| Status |
Public on Oct 16, 2014 |
| Title |
KSHV Transcriptome at 72hpi in TIVE |
| Sample type |
SRA |
| |
|
| Source name |
TIVE cells infected with KSHV
|
| Organism |
Human gammaherpesvirus 8 |
| Characteristics |
cell type: Telomerase Immortalized Vascular Endothelial (TIVE) cells
infected with: KSHV virus
time point: 72hpi
|
| Treatment protocol |
human TIVE cells were infected with KSHV virus prepared from BCBL-1 cells at the MOI of 10.
|
| Growth protocol |
human TIVE cells were cultured in complete medium containing 10% FBS at 37oC in humidified chamber with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Infected cells were cultured for indicated time followed by washing them to remove virus attached to the cell surface. RNA was extracted by standard RNA extraction protocol
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The libraries were run on Illumina Hi-seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Henomic Workbech 7.0 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to KSHV data base sequence to calculate the RPKM values of each gene using CLC Workbech 7.0
Genome_build: NCBI genome build of KSHV, accession number NC_009333
Supplementary_files_format_and_content: Comma separated (CSV) files have RPKM values of each genes at respective time points.
|
| |
|
| Submission date |
Oct 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Subhash C Verma |
| E-mail(s) |
scverma@medicine.nevada.edu
|
| Phone |
775-682-6743
|
| Organization name |
University of Nevada, Reno
|
| Department |
Microbiology and Immunology
|
| Lab |
Verma Lab
|
| Street address |
1664 N Virginia Street, MS 320
|
| City |
Reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL17680 |
| Series (2) |
| GSE62342 |
Transcriptome Analysis of KSHV during de novo primary infection of endothelial (TIVE) cells |
| GSE62344 |
Transcriptome Analysis of KSHV during de novo primary infection of human B-and endothelial-cells |
|
| Relations |
| BioSample |
SAMN03108573 |
| SRA |
SRX732913 |
