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Sample GSM739783 Query DataSets for GSM739783
Status Public on Dec 31, 2012
Title MeOH_4h_replicate_3
Sample type RNA
 
Source name Caco-2 cells, MeOH, 4h
Organism Homo sapiens
Characteristics cell line: Caco-2
cell type: colon adenocarcinoma cells
differentiation state: differentiated
treatment: MeOH
treatment duration: 4h
Treatment protocol Differentiated Caco-2 cells were exposed to different concentrations of MC-RR or MC-LR treatment in free FCS culture medium for either 4 or 24 hours.
Growth protocol The Caco-2 cells (ATCC HTB-37), passages 30-33, were cultured in GlutaMAX minimum essential medium (MEM) with 1% non-essential amino acids, penicillin (50 IU/mL) and streptomycin (50 μg/mL) (InVitrogen) and supplemented with 10% fetal calf serum (FCS, InVitrogen). Cells were grown in 75 cm² flasks at 37°C in an atmosphere containing 5% CO2 and subcultured twice a week. To obtain differentiated Caco-2 cells, the cells were seeded into 12-wells plates (60× 103 cells/cm²) and maintained 24 days in 10% FCS culture medium with a medium change every 2 or 3 days.
Extracted molecule total RNA
Extraction protocol Total RNA of each replicate was extracted by standard TRIzol RNA extraction protocol (InVitrogen). The RNA integrity and quantity were assessed with the Agilent 2100 Bioanalyzer. Only the RNA samples with a RIN (RNA Integrity Number) above 8 were considered further for the transcriptomic study.
Label Cy3
Label protocol RNA samples were converted to aminoallyl-RNA (aRNA) using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) prior to labeling with either Cy3 or Cy5 dye using the Quick Amp Labeling Kit (Agilent).
 
Hybridization protocol Hybridization, washing and drying of the microarray were performed in a HS4800 Pro Hybridization station (Tecan). Washing was performed with the Gene Expression Wash Pack (Agilent) and drying with the Stabilization and Drying Solution (Agilent).
Scan protocol The slides were scanned with an Innoscan 900AL scanner (Innopsys, Toulouse, France).
Description MeOH_4h_D0_cy3_8
Data processing The raw data were normalized and scaled with the lowess algorithm. The median sample (median of all samples) were used for fitting of a non-linear normalization curve.
 
Submission date Jun 09, 2011
Last update date Dec 31, 2012
Contact name Perrine Zeller
E-mail(s) perrine.zeller@anses.fr
Organization name ANSES
Department UTC
Lab Fougères
Street address la haute marche-javené
City Fougères
ZIP/Postal code 35302
Country France
 
Platform ID GPL4133
Series (1)
GSE29861 Comparison of the MC-LR and MC-RR effects on Caco-2 cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 60684.80315
2 31.46837537
3 25.76364558
4 28.19809127
5 30.83181613
6 30.57663432
7 25.15712064
8 23.91566194
9 26.89611352
10 26.34718833
11 33.45270894
12 232.8044791
13 44.41521573
14 187.0994106
15 57.11665137
16 1964.192415
17 72.56871255
18 191.8677223
19 56286.87705
20 58.09468061

Total number of rows: 45220

Table truncated, full table size 779 Kbytes.




Supplementary file Size Download File type/resource
GSM739783_2010-02-17_11h58m59_251485052388_8cy3-64cy5.txt.gz 11.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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