NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1976554 Query DataSets for GSM1976554
Status Public on Mar 01, 2016
Title Tomato_THP1_1
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_1.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

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
1 14.46117703
2 4.930141709
3 4.823179213
4 10.23119774
5 5.052093122
6 4.823179213
7 4.919097
8 5.052093122
9 15.03925406
10 11.07703904
11 6.300636518
12 12.05944678
13 6.435512211
14 4.886957016
15 4.844341886
16 4.797730252
17 8.518795851
18 8.736199654
19 5.796947954
20 10.84795122

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap