|
| Status |
Public on Oct 16, 2014 |
| Title |
BAC36 Transcriptome at 48hpi |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs infected with KSHV-BAC
|
| Organism |
Human gammaherpesvirus 8 |
| Characteristics |
cell type: peripheral blood mononuclear cells (PBMCs)
infected with: wild type KSHV
time point: 48hpi
|
| Treatment protocol |
human PBMCs were infected with KSHV virus prepared from 293L cells maintaining BAC36 or BAC36-delORF50 completed with DsRed-ORF59 at MOI of 10.
|
| Growth protocol |
Decoded human peripheral blood mononuclear cells (PBMCs) were purchased from ReachBioo and infected with KSHV virus
human PBMCs were cultured in complete RPMI 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 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) |
| GSE62339 |
Transcriptome Analysis of BAC36 and ORF59 deleted BAC36 during de novo primary infection of human B cells (PBMCs) |
| GSE62344 |
Transcriptome Analysis of KSHV during de novo primary infection of human B-and endothelial-cells |
|
| Relations |
| BioSample |
SAMN03108553 |
| SRA |
SRX732901 |
