|
| Status |
Public on Feb 16, 2019 |
| Title |
48Hr mutant rescue-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organisms |
Homo sapiens; Human gammaherpesvirus 8 |
| Characteristics |
cell line: iSLK
latent infection: Mutant rescue
time point: 48 hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed using Trizol and RNA extracted using Zymo RNA extraction kit as per protocol mentioned by manufacturer.
Libraries were prepared by the qb3 facility at UC Berkeley.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Wild type
|
| Data processing |
Reads were analyzed using FastQC and trimmed using TrimGalore using default parameters.
The trimmed reads were aligned to both the viral (NC_009333.1) and host genomes (hg19) using STAR aligner (ver2.5.3a).
The aligned reads were counted using htseq-counts.
Genome_build: hg19 (GRCh37), NC_009333.1
Supplementary_files_format_and_content: *.txt: Text files with read counts for human and viral genes generated by htSeq-counts.
|
| |
|
| Submission date |
Feb 14, 2019 |
| Last update date |
Feb 17, 2019 |
| Contact name |
Britt Glaunsinger |
| Organization name |
UC Berkeley
|
| Street address |
565 Li Ka Shing Center
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL25719 |
| Series (2) |
| GSE126602 |
RNA sequencing analysis to identify gene targets of Kaposi's sarcoma herpesvirus (KSHV) ORF24 |
| GSE126603 |
An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi’s sarcoma-associated herpesvirus |
|
| Relations |
| BioSample |
SAMN10953185 |
| SRA |
SRX5382899 |
