|
| Status |
Public on Jul 14, 2006 |
| Title |
CaCo2-SF-0_c |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
caco-2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
Caco-2 cells, originating from a human colorectal carcinoma (HTB-37)
|
| Biomaterial provider |
American Type Culture Collection (Manassas, VA)
|
| Treatment protocol |
Fully differentiated CaCo-2 cells were submitted to Iron and serum free medium (IMDM+serum complement) (SF-0)
|
| Growth protocol |
CaCo-2 cells were grown in DMEM containing 10% FBS, 1X non-essential amino-acids, 2mM L-glutamine and 100 IU/ml antibiotics (penicillin and streptomycin) (all reagents were purchased from Gibco BRL) in a humidified atmosphere of 95% air and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRI REAGENT kit (Sigma)
|
| Label |
cy5
|
| Label protocol |
Agilent Low RNA Input Fluorescent Linear Amplification Kit (p/n 5184-3523)
|
| |
|
| Channel 2 |
| Source name |
pool of all used RNA
|
| Organism |
Homo sapiens |
| Characteristics |
Caco-2 cells, originating from a human colorectal carcinoma (HTB-37)
|
| Biomaterial provider |
American Type Culture Collection (Manassas, VA)
|
| Treatment protocol |
Pool of all extracted RNAs from fully differentiated CaCo-2 cells submitted to various treatments:
(1) DMEM 10% FBS (DMEM-FBS)
(2) DMEM 10% FBS and 100 µM Hemin (DMEM-Hemin)
(3) Iron and serum free medium (IMDM+serum complement) (SF-0)
(4) Iron and serum free medium + 4.4 µM FAC (ferric ammonium citrate) (SF-FAC)
|
| Growth protocol |
CaCo-2 cells were grown in DMEM containing 10% FBS, 1X non-essential amino-acids, 2mM L-glutamine and 100 IU/ml antibiotics (penicillin and streptomycin) (all reagents were purchased from Gibco BRL) in a humidified atmosphere of 95% air and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRI REAGENT kit (Sigma)
|
| Label |
cy3
|
| Label protocol |
Agilent Low RNA Input Fluorescent Linear Amplification Kit (p/n 5184-3523)
|
| |
|
| |
| Hybridization protocol |
Agilent oligonucleotide microarray in situ Hybridization Plus kit (p/n 5184-3568).
|
| Scan protocol |
Agilent dual laser DNA microarray scanner (p/n G2566AA) and Feature Extraction software 7.5 (p/n G2567AA)
|
| Description |
Each sample were labelled with cy5 and a pool of each sample was constituted and labelled with cy3
|
| Data processing |
adjustment local background subtraction and global background Normalization method : Linear&Lowess method. only features with a Signal-to-Noise Ratio (SNR) in at least one channel ≥ 2.6 were used for further analysis and saturated features (50% of pixels > saturation threshold, 65502) or non uniform features were discarded.
|
| |
|
| Submission date |
Nov 04, 2005 |
| Last update date |
Jul 14, 2006 |
| Contact name |
chicault celine |
| E-mail(s) |
celine.chicault@univ-rennes1.fr
|
| Organization name |
UMR6061
|
| Street address |
2 avenue du Pr Leon Bernard
|
| City |
rennes |
| ZIP/Postal code |
35043 |
| Country |
France |
| |
|
| Platform ID |
GPL887 |
| Series (1) |
| GSE3573 |
Transcriptional effect of various iron treatments on Caco-2 cells. |
|
