|
| Status |
Public on Aug 09, 2016 |
| Title |
Mock 24 hs replicate A |
| Sample type |
SRA |
| |
|
| Source name |
A549_Mock 24 hs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
infected with: mock
time point: 24 hours post infection
|
| Treatment protocol |
The cells where infected with Dengue virus 2 or Mock 1 h at 37°C (MOI 10)
|
| Growth protocol |
Standard conditions for A549 infected cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was purified using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data column: M24A
|
| Data processing |
Base
Sequence reads were mapped to Homo sapiens UCSC hg19 genome using TopHat v2.1.1 with default parameters
Count tables for different feature levels were obtained from bam files using custom R v3.0.2 scripts.
Differential gene expression was estimated using edgeR package version 3.4.2 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
The transcriptome was partitioned into subgenic joint features called bins and labeled as exon-bin, intron-bin or alternative-splicing (AS) bins. In addition AS-bins were further classified as exon skipping (ES), 5’ or 3’ alternative (5´alt, 3´alt), intron retention (IR) or multiple. Bins from monoexonic genes, with mean count values lower than 5 reads per condition and rd bin / rd gen lower than 0.05 were discarded.
COPIAR DE MyM
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Comprehensive spreadsheets with the results of the analysis of differential splicing detailed above
|
| |
|
| Submission date |
Jul 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrea Gamarnik |
| E-mail(s) |
agamarnik@leloir.org.ar
|
| Organization name |
Fundacion Instituto Leloir
|
| Street address |
Av. Patricias Argentinas 435
|
| City |
Ciudad Autonoma de Buenos Aires |
| ZIP/Postal code |
C1405BWE |
| Country |
Argentina |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE84285 |
Genome-wide analysis of Dengue virus 2 infected cells |
|
| Relations |
| BioSample |
SAMN05375347 |
| SRA |
SRX1934569 |
