|
| Status |
Public on Dec 31, 2012 |
| Title |
MeOH_24h_replicate_5 |
| Sample type |
RNA |
| |
|
| Source name |
Caco-2 cells, MeOH, 24h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Caco-2
cell type: colon adenocarcinoma cells
differentiation state: differentiated
treatment: MeOH
treatment duration: 24h
|
| 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 |
Cy5
|
| 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_24h_D0_cy5_79
|
| 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 |
|
