|
| Status |
Public on Nov 30, 2015 |
| Title |
E3 X H3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
TEC + T cell non-infected supernatant (CEM)-replicate 3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THF
supernatant from t cell line: CEM
|
| Treatment protocol |
Thymic Epithelial Cell (TEC) were in contact with the supernatant from CEM, CIB or C91PL for 1.5 hour at 37°C and then washed with PBS.
|
| Growth protocol |
All cells were cultivated in RPMI (Sigma) supplemented with 10% of fetal bovine serum (FBS) (GIBCO) in 5% of CO2, 37°C in humidity and for CIB we supplemented the medium with 50 units/mL of IL-2 (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from TECs was extracted with TRIreagent (Sigma-Aldrich) according to the manufacturer’s protocol. Total RNA concentration and quality was measured using NanoDrop (Thermo Scientific) and 2100 Bioanalyzer (Agilent Technologies), respectively.
|
| Label |
Cy3
|
| Label protocol |
We used 400 ng of total RNA of three independent samples for each condition, using two-color hybridizations with dye-swap in a 4 X 44K Agilent Whole Human Gene Microarray (G4112F, Agilent Technologies). Labeling was performed according to the manufacturer's instructions (Agilent Technologies).
|
| |
|
| Channel 2 |
| Source name |
TEC without supernatant-replicate 3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THF
supernatant from t cell line: NONE
|
| Treatment protocol |
Thymic Epithelial Cell (TEC) were in contact with the supernatant from CEM, CIB or C91PL for 1.5 hour at 37°C and then washed with PBS.
|
| Growth protocol |
All cells were cultivated in RPMI (Sigma) supplemented with 10% of fetal bovine serum (FBS) (GIBCO) in 5% of CO2, 37°C in humidity and for CIB we supplemented the medium with 50 units/mL of IL-2 (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from TECs was extracted with TRIreagent (Sigma-Aldrich) according to the manufacturer’s protocol. Total RNA concentration and quality was measured using NanoDrop (Thermo Scientific) and 2100 Bioanalyzer (Agilent Technologies), respectively.
|
| Label |
Cy5
|
| Label protocol |
We used 400 ng of total RNA of three independent samples for each condition, using two-color hybridizations with dye-swap in a 4 X 44K Agilent Whole Human Gene Microarray (G4112F, Agilent Technologies). Labeling was performed according to the manufacturer's instructions (Agilent Technologies).
|
| |
|
| |
| Hybridization protocol |
Hybridization and washing were performed according to the manufacturer's instructions (Agilent Technologies).
|
| Scan protocol |
Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA).
|
| Description |
Biological replicate 3 of 3, technical replicate 1 of 2. TEC + T cell non-infected supernatant (CEM)/TEC without supernatant
|
| Data processing |
Intensities were extracted using the Agilent Feature Extraction software (AFE, version A.9.5.3) with standard protocols and options. The pre-processing and differential expression analysis of gene expression data were performed in the R programming environment and processed using Bioconductor (http://www.bioconductor.com) Agi4x44PreProcess library. Normalized data were scaled by the quantile method and filtered to 1) maintain intensities within the dynamic range of the scanner (elimination of saturated points); and 2) retain genetic data of good quality. The library of the Bioconductor hgug4112a.db was used to assign the access code for the gene (ENTREZ ID) corresponding to each probe Agilent. Differential expression was analyzed with the limma library in empirical Bayesian methods.
|
| |
|
| Submission date |
Sep 17, 2015 |
| Last update date |
Nov 30, 2015 |
| Contact name |
Leandra Linhares Lacerda |
| E-mail(s) |
leandralacerda@gmail.com
|
| Phone |
55-21-25621223
|
| Organization name |
Oswaldo Cruz Foundation
|
| Department |
Oswaldo Cruz Institution
|
| Lab |
Laboratory on Thymus Research
|
| Street address |
Av. Brasil 4365 pav 26 sala 506 Manguinhos
|
| City |
Rio de Janeiro |
| State/province |
RJ |
| ZIP/Postal code |
21040-360 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE73170 |
Thymic Epithelial Cells with Human T cell Leukemia Virus type 1 (HTLV-1) Infected T cell supernatant (with or without supernatant) |
| GSE74591 |
Thymic Epithelial Cells with Human T cell Leukemia Virus type 1 (HTLV-1) Infected T cell supernatant |
|
