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Sample GSM81967 Query DataSets for GSM81967
Status Public on Jul 14, 2006
Title CaCo2-SF-0_a
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.

Data table header descriptions
ID_REF
VALUE Log10 Ratio of processed Cy5 (red) signal to processed Cy3 (green)
PValueLogRatio p-value of the log ratio as determined by Agilent error model
gProcessedSignal normalized and background subtracted Cy3 (green) signal
rProcessedSignal normalized and background subtracted Cy5 (red) signal
gMeanSignal raw Cy3 (green)
rMeanSignal raw Cy5 (red)

Data table
ID_REF VALUE PValueLogRatio gProcessedSignal rProcessedSignal gMeanSignal rMeanSignal
1 -1.03E+00 4.97E-28 6.63E+03 6.12E+02 1.26E+03 2.02E+02
2 -6.37E-01 4.83E-01 1.19E+02 2.74E+01 1.53E+02 7.19E+01
3 -1.65E-01 5.82E-01 2.30E+02 1.57E+02 1.75E+02 9.96E+01
4 -8.74E-02 1.80E-01 1.48E+03 1.21E+03 3.87E+02 3.32E+02
5 -1.19E-01 1.43E-01 1.00E+03 7.63E+02 3.08E+02 2.34E+02
6 -2.18E-01 6.19E-01 1.65E+02 1.00E+02 1.61E+02 8.84E+01
7 -1.37E+00 2.72E-31 6.82E+03 2.88E+02 1.30E+03 1.30E+02
8 -9.45E-02 7.93E-02 3.00E+03 2.41E+03 6.41E+02 6.03E+02
9 -9.37E-02 8.99E-02 2.59E+03 2.08E+03 5.72E+02 5.31E+02
10 2.17E-01 4.36E-01 1.60E+02 2.63E+02 1.61E+02 1.22E+02
11 -3.64E-02 8.52E-01 3.13E+02 2.88E+02 1.88E+02 1.27E+02
12 -1.13E-01 7.14E-01 2.11E+02 1.63E+02 1.70E+02 1.00E+02
13 3.29E-02 8.96E-01 2.20E+02 2.37E+02 1.72E+02 1.16E+02
14 -1.38E+00 1.55E-31 7.35E+03 3.08E+02 1.39E+03 1.35E+02
15 -4.98E-02 3.20E-01 6.50E+03 5.79E+03 1.25E+03 1.35E+03
16 -2.46E-02 7.35E-01 1.09E+03 1.03E+03 3.19E+02 2.91E+02
17 8.80E-02 9.26E-01 5.38E+01 6.58E+01 1.40E+02 8.16E+01
18 -6.64E-02 2.82E-01 1.65E+03 1.41E+03 4.14E+02 3.80E+02
20 -2.88E-01 7.53E-01 8.46E+01 4.36E+01 1.47E+02 7.73E+01
21 -1.34E+00 2.31E-31 7.51E+03 3.42E+02 1.42E+03 1.44E+02

Total number of rows: 22153

Table truncated, full table size 1298 Kbytes.




Supplementary data files not provided

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