|
| Status |
Public on Oct 16, 2014 |
| Title |
KSHV Transcriptome in virions produced from 293L with BAC36 deleted ORF59 complemented with DsREd ORF59 |
| Sample type |
SRA |
| |
|
| Source name |
KSHV virions
|
| Organism |
Human gammaherpesvirus 8 |
| Characteristics |
host cells: 293L with BAC36 deleted ORF59 complemented with DsREd ORF59
sample type: total RNA packaged into virions particles
virus genotype/variation: BAC36-delORF59 virus complemented with DSRED ORF59
|
| Treatment protocol |
Total RNA was treated with DNAse to eliminate DNA contamination.
|
| Growth protocol |
Virions were purfied after induction of respective cells. purified virions were treated with micrococcal nuclease to eliminate surface attached RNA. Total RNA was extracted byTRIzol method.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted extracted was done by TRIzol method and depleted for contaminating DNA by treatment with DNAse
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) |
| GSE62343 |
Transcriptome Analysis of KSHV virions produced from BCBL1 and BAC36 in 293L cells |
| GSE62344 |
Transcriptome Analysis of KSHV during de novo primary infection of human B-and endothelial-cells |
|
| Relations |
| BioSample |
SAMN03108582 |
| SRA |
SRX732917 |
