|
| Status |
Public on Mar 13, 2024 |
| Title |
VPM+NaB rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HH514-16 P3HR-1-derived Epstein-Barr virus-positive Burkitt lymphoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
drug treatment: valpromide 10 mM + sodium butyrate 3 mM
treatment time: 6 hour
|
| Treatment protocol |
Cells at 1 x 10^6 cells/mL were treated with drugs for 6 hours.
|
| Growth protocol |
Cells were maintained in 5% CO2 at 37°C in RPMI 1640 supplemented with 8% fetal calf serum. Cells were subcultured to 3-4 x 10^5 cells/mL 2 days prior to drug treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Qiagen Rneasy Mini kit.
Strand-specific sequencing libraries were produced from purified total RNA samples by the Illumina TruSeq stranded protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor and low-quality sequences using Trimmomatic Galaxy version 0.36.5.
Paired reads were mapped to an indexed hg38 transcriptome
Quantified was performed using Salmon v0.12.0 with parameter --validateMappings
Genome_build: hg38
Supplementary_files_format_and_content: Quantification files from Salmon (TPM)
|
| |
|
| Submission date |
Aug 13, 2019 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Kelly Gorres |
| Organization name |
University of Wisconsin-La Crosse
|
| Department |
Chemistry & Biochemistry
|
| Street address |
1725 State St, Cowley 4015
|
| City |
La Crosse |
| State/province |
WI |
| ZIP/Postal code |
54601 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE135794 |
Changes in cellular transcriptome in response to inhibitors of Epstein-Barr virus |
|
| Relations |
| BioSample |
SAMN12567624 |
| SRA |
SRX6709586 |
