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Sample GSM1888096 Query DataSets for GSM1888096
Status Public on Nov 30, 2015
Title F3 X E3- DYE-SWAP ARRAY 17
Sample type RNA
 
Channel 1
Source name TEC + T cell-infected supernatant (CIB)-replicate 3
Organism Homo sapiens
Characteristics cell line: THF
supernatant from t cell line: CIB
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 + 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 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 2 of 2. TEC + T cell-infected supernatant (CIB)/TEC + T cell non-infected supernatant (CEM)
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)
GSE73169 Thymic Epithelial Cells with Human T cell Leukemia Virus type 1 (HTLV-1) Infected T cell supernatant (CEM, CIB, C91PL)
GSE74591 Thymic Epithelial Cells with Human T cell Leukemia Virus type 1 (HTLV-1) Infected T cell supernatant

Data table header descriptions
ID_REF
VALUE log2 Cy3/Cy5

Data table
ID_REF VALUE
A_24_P66027 0.091
A_23_P212522 -0.052
A_24_P9671 0.081
A_24_P801451 -0.123
A_32_P30710 0.765
A_24_P704878 0.14
A_32_P86028 0.439
A_23_P65830 0.064
A_23_P109143 0.234
A_24_P391591 0.214
A_24_P835500 0.205
A_23_P67555 0.43
A_24_P286412 -0.672
A_23_P202696 0.239
A_23_P124837 0.099
A_24_P329635 -0.025
A_23_P148439 0.075
A_23_P203819 0.038
A_23_P253052 0.276
A_32_P139302 0.298

Total number of rows: 29628

Table truncated, full table size 550 Kbytes.




Supplementary file Size Download File type/resource
GSM1888096_Array_18.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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