|
| Status |
Public on Oct 16, 2014 |
| Title |
KSHV Transcriptome at 4hpi in CD14+ cells |
| Sample type |
SRA |
| |
|
| Source name |
HumanCD14+ cells infected with KSHV
|
| Organism |
Human gammaherpesvirus 8 |
| Characteristics |
cell type: human CD14+ cells
infected with: Kaposi's sarcoma-associated herpesvirus (KSHV)
time point: 4hpi
|
| Treatment protocol |
human CD14+ cells were infection with KSHV virus prepared from BCBL-1 cells and infected at MOI of 10.
|
| Growth protocol |
Decoded human CD14+ cells were purchased from ReachBioo were infected with KSHV virus
human CD14+ cells were cultured in complete IMDM 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 with to remove virua 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) |
| GSE62340 |
Transcriptome Analysis of KSHV during de novo primary infection of human CD14+ cells |
| GSE62344 |
Transcriptome Analysis of KSHV during de novo primary infection of human B-and endothelial-cells |
|
| Relations |
| BioSample |
SAMN03108563 |
| SRA |
SRX732918 |
