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Sample GSM1140838 Query DataSets for GSM1140838
Status Public on Jul 22, 2013
Title Azathioprine 100nM, biological rep1
Sample type RNA
 
Source name Jurkat, P16
Organism Homo sapiens
Characteristics passage: P16
cell type: Human T cell
agent: Azathioprine 100nM
cell line: Jurkat, Clone E6-1
Treatment protocol Jurkat cells (passage number 16 to 20) were seeded in 2.7 ml medium per well in 6-well plates (750,000 cells/well) . After growing the cells for 20 hours, exposure was initiated by adding 0.3 ml medium containing non-cytotoxic concentration of the compounds or vehicle controls. Subsequently, cells were exposed to the compounds for 6 h. The final DMSO concentration in the medium was 0.1% (v/v) for all the samples. Each exposure was performed in quadruplicate at four different days.with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).
Growth protocol The Jurkat cells were grown in RPMI-1640 medium supplemented with 10% heat inactivated Fetal Calf Serum (FCS), 2 mM glutamine, 1 mM sodium pyruvate, 1 mM non-essential amino acids, 100 U/ml penicillin, and 100 µg/ml streptomycin. Cells were cultured at 37 °C with 5% CO2 in a humidified atmosphere. The medium was refreshed every 2 days.
Extracted molecule total RNA
Extraction protocol RNA was isolated by using Qiagen QIAshredder kit according to the manufacturer’s protocol. RNA purification was done using Qiagen miRNeasy Mini kit.
Label biotin
Label protocol cDNA synthesis and subsequent synthesis of biotin-labeled cRNA was performed using GeneChip One-Cycle Target Labeling and Control Reagents including the One-Cycle cDNA Synthesis Kit, Poly-A RNA Control Kit, Sample Cleanup Module, IVT Labeling Kit, and Hybridization Control Kit (all from Affymetrix) according to the manufacturer’s protocol.
 
Hybridization protocol cRNAs were hybridized to the arrays for 16 hours at 45 °C (GeneChip Hybridization Oven 640; Affymetrix). Washing and staining were done by using GeneChip hybridization station, Fluidics Station 450, Affymetrix.
Scan protocol GeneChips were scanned by Affymetrix GeneChip Scanner 3000 7G.
Data processing Raw data were extracted using GeneChip Operating Software (Affymetrix). In order to filter out probes with sub-optimal specificity for the encoding genes, custom CDF files were generated from the raw data files, by using the R package available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.asp. Then robust multichip average (RMA) normalization was applied to the complete dataset (Bioconductor). BioConductor packages were used for the quality control of the microarray data (www.arrayanalysis.org).
 
Submission date May 14, 2013
Last update date Jul 22, 2013
Contact name Jia Shao
E-mail(s) [email protected]
Organization name RIKILT-Institute of food safety
Department TE
Street address Akkermaalsbos 2
City Wageningen
ZIP/Postal code 6708 WB
Country Netherlands
 
Platform ID GPL16311
Series (1)
GSE46909 Expression data from human Jurkat T cells exposed to 31 compounds

Data table header descriptions
ID_REF
VALUE RMA normalized microarray data

Data table
ID_REF VALUE
100009676_at -0.09804369
10000_at 0.083974931
10001_at -0.268851834
10002_at 0.023158483
10003_at -0.210373831
100048912_at 0.518560786
100049716_at 0.247505563
10004_at 0.093485509
10005_at -0.15158176
10006_at 0.192350711
10007_at -0.195747816
10008_at 0.123823385
100093630_at -0.050774119
10009_at -0.124952235
1000_at -0.103877311
100101467_at 0.200822022
100101938_at 0.597691518
10010_at -0.096553713
100113407_at -0.203734669
10011_at -0.187648851

Total number of rows: 19070

Table truncated, full table size 400 Kbytes.




Supplementary file Size Download File type/resource
GSM1140838_AZA_100nM_ex1.CEL.gz 5.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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