|
| Status |
Public on Mar 01, 2016 |
| Title |
Tomato_THP1_3 |
| Sample type |
RNA |
| |
|
| Source name |
THP-1 (TIB-202) Tomato virus
|
| Organism |
Homo sapiens |
| Characteristics |
virus: vvdd-tdTomato
cell line: THP-1 (TIB-202)
|
| Treatment protocol |
Cells were infected with 0.1 pfu/cell of virus (vvdd-tdTomato control virus or vvdd-tdTomato-hDAI virus) for 16 hours. Mock samples were treated with PBS only. 2% growth medium was used as treatment medium.
|
| Growth protocol |
HS294T cells were cultured on 6-well plates 1,5x10^6 cells/well in 10% DMEM (with 1% L-glutmanine and 1% Pen-Strep) over night. THP-1 cells were cultured in T75 flasks in 10% RPMI-1640 (with 1% L-glutmanine, 1% Pen-Strep and 0,05 mM 2-Mercaptoethanol).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified with RNeasy Plus Mini kit (Qiagen, Venlo, NL) according to manufacturer´s instructions.
|
| Label |
Cy3
|
| Label protocol |
Independent pools of two RNA samples each (total of 600 ng) were labeled using T7 RNA polymerase amplification method (Low Input Quick Amp Labeling Kit, Agilent Technologies, Inc., Santa Clara, CA, USA), according to the instructions of the manufacturer. cRNAs were then labeled with Cy3 and Cy5 dyes (Agilent Technologies)
|
| |
|
| Hybridization protocol |
cRNAs were hybridized to the Agilent 2-color 60-mer oligo arrays (Agilent SurePrint G3 Human GE 8x60K).
|
| Scan protocol |
The slides were scanned with Agilent Microarray Scanner G2505C (Agilent Technologies) and the raw intensity values were obtained with the Feature Extraction software, version 11.0.1.1 (Agilent Technologies). Raw data was quality checked according to the Agilent standard procedures.
|
| Description |
US11263921_253949430778_S01_GE2_1105_Oct12_2_2.txt
THP1 cells with Tomato virus
|
| Data processing |
Data pre-processing and differential expression analysis of the gene expression data were done in R. First, the probe profile expression data were normalized using quantile normalization and corrected for batch processing effects using ComBat. Next, after mapping from probsets to Ensemble gene IDs, the differentially expressed genes (DE genes) between pre- and post-treatment samples were identified using limma. Finally, functional categorization of DE genes was performed using a novel R-based package namely BACA. It queries the DAVID knowledgebase and build a charts showing multiple enrichment analysis results across different conditions/treatments.
For the analysis using the limma package, genes were defined as being differentially expressed after satisfying a minimum fold-change of ±1.5 and a maximum Benjamini-Hochberg adjusted p-value of 0.01.
|
| |
|
| Submission date |
Dec 21, 2015 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Dario Greco |
| E-mail(s) |
dario.greco@tuni.fi
|
| Organization name |
Tampere University
|
| Department |
Faculty of Medicine and Health Technology
|
| Lab |
Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)
|
| Street address |
Arvo ylpön Katu 34
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE76208 |
Effect of human DAI expressed by an oncolytic vaccinia virus on the gene expression of tumor cells (HS294T) and monocytes (THP-1). |
|
| Relations |
| Reanalyzed by |
GSE113533 |
