|
| Status |
Public on Sep 01, 2016 |
| Title |
72 h DENV1 infection Total cell lysate ribosome profiling (rep 2) |
| Sample type |
SRA |
| |
|
| Source name |
Huh7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7 cells
protocol: 72 h DENV1 infection
compartment: Total cell lysate
analysis: ribosome profiling
replicate: rep 2
strain: DENV1 (EU081230.1)
|
| Treatment protocol |
Infection with DENV or treatment with interferon
|
| Growth protocol |
Cultured in DMEM + 10% FBS, 37C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pre-treatment with 180 uM cycloheximide for 30s. PBS wash. For fractionated cells, release cytosol with digitonin. Extract remaining sample with dodecyl maltoside.
NEB Directional Small RNA kit
PNK end polishing, linker ligation, reverse transcription, PCR amplification
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Library strategy: Ribo-Seq
processed data file: DENVExpression-wholecell.xlsx
|
| Data processing |
Read trimming with cutadapt
Map reads to transcriptome with Bowtie (no mismatches)
Quantify translation as RPKM
Genome_build: hg19 (transcripts selected using Tophat/Cufflinks) + EU081177.1 + EU081230.1 + M29095.1
Supplementary_files_format_and_content: Excel spreadsheet indicating RPKM values
|
| |
|
| Submission date |
Jun 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
David Reid |
| Organization name |
Duke University
|
| Department |
Biochemistry
|
| Lab |
Nicchitta
|
| Street address |
436 Nanaline Duke Bldg., Box 3709 DUMC
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE69602 |
Ribosome profiling analysis of Dengue Virus |
|
| Relations |
| BioSample |
SAMN03763477 |
| SRA |
SRX1050410 |
