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Sample GSM1841146 Query DataSets for GSM1841146
Status Public on Aug 01, 2015
Title non-fortified carrots 3
Sample type RNA
 
Channel 1
Source name Caco-2 colorectal adenocarcinoma cells, non-fortified carrots, Replicate 3
Organism Homo sapiens
Characteristics cell line: Caco-2 (HTB-37, ATCC)
tissue: Colon
cell type: epithelial
gender/age: Male/72 years adult
Treatment protocol Cells were seeded in 6-well culture plates for 24 h. After that, growing medium was replaced by medium containing the extract from iodine-biofortified lettuce/carrot and the extract from non-fortified lettuce/carrot. In all studies, at least 4 wells were examined per treatment. Experiments were repeated 3 times.
Growth protocol Cells were cultured in an incubator, under controlled conditions (temperature, 37°C; air, 95%; CO2, 5%), in Eagle's Minimum Essential Medium (Sigma), with fetal bovine serum (FBS) (Gibco) to a final concentration of 20%, according to ATCC procedure.
Extracted molecule total RNA
Extraction protocol Lettuce and carrot were cultivated and fertilizated with KI as described by Kopeć et al. (2015). The iodine concentration was 0.50 mg/100 g dry mass (d.m.) for biofortified lettuce and 0.12 mg/100 g d.m. for control lettuce (Kopeć et al. 2015). 10 g of fresh lettuce was crushed using a homogenizer (CAT type X 120, USA) and next transferred to the Erlenmaier flask with hot water. Lettuce materials were extracted by shaking (Elpan, water bath shaker type 357, Poland) at 100°C for 2 hours, and next the solution was centrifuged (Centrifuge type MPW-340, Poland). Then, a part of the extracts was used for iodine measurement and other parts were stored at -80 °C for cell culture studies.
Label Cy5
Label protocol According to the manufacturer's protocol
 
Channel 2
Source name Colorectal adenocarcinoma
Organism Homo sapiens
Characteristics cell line: Caco-2 (HTB-37, ATCC)
tissue: Colon
cell type: epithelial
gender/age: Male/72 years adult
Treatment protocol Cells were seeded in 6-well culture plates for 24 h. After that, growing medium was replaced by medium containing the extract from iodine-biofortified lettuce/carrot and the extract from non-fortified lettuce/carrot. In all studies, at least 4 wells were examined per treatment. Experiments were repeated 3 times.
Growth protocol Cells were cultured in an incubator, under controlled conditions (temperature, 37°C; air, 95%; CO2, 5%), in Eagle's Minimum Essential Medium (Sigma), with fetal bovine serum (FBS) (Gibco) to a final concentration of 20%, according to ATCC procedure.
Extracted molecule total RNA
Extraction protocol Lettuce and carrot were cultivated and fertilizated with KI as described by Kopeć et al. (2015). The iodine concentration was 0.50 mg/100 g dry mass (d.m.) for biofortified lettuce and 0.12 mg/100 g d.m. for control lettuce (Kopeć et al. 2015). 10 g of fresh lettuce was crushed using a homogenizer (CAT type X 120, USA) and next transferred to the Erlenmaier flask with hot water. Lettuce materials were extracted by shaking (Elpan, water bath shaker type 357, Poland) at 100°C for 2 hours, and next the solution was centrifuged (Centrifuge type MPW-340, Poland). Then, a part of the extracts was used for iodine measurement and other parts were stored at -80 °C for cell culture studies.
Label Cy3
Label protocol According to the manufacturer's protocol
 
 
Hybridization protocol According to the manufacturer's protocol
Scan protocol Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software.
Description Biological replicate 3 of 3. Cells treated with the extract of non-fortified carrots
Data processing Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.
 
Submission date Jul 31, 2015
Last update date Aug 01, 2015
Contact name Magdalena Łój
E-mail(s) magda.loj@gmail.com
Organization name Warsaw University of Life Sciences
Department Department of Physiological Sciences
Street address Nowoursynowska 166
City Warsaw
ZIP/Postal code 02-787
Country Poland
 
Platform ID GPL17077
Series (1)
GSE71605 Global changes in gene expression in Caco-2 cell line by treatment with extract from iodine-biofortified carrot and lettuce

Data table header descriptions
ID_REF
VALUE Linear Lowess normalized test/reference

Data table
ID_REF VALUE
GE_BrightCorner -0.041620217
DarkCorner -0.12914343
A_23_P117082 -0.09869952
A_33_P3246448 -0.3894339
A_33_P3318220 -0.39121503
A_33_P3236322 -0.77414286
A_33_P3319925 -0.6589104
A_21_P0000509 -0.33256152
A_21_P0000744 0.615158
A_24_P215804 0.1106872
A_23_P110167 -0.18220322
A_33_P3211513 0.036484204
A_23_P103349 0.41332886
A_32_P61480 -0.4046138
A_33_P3788124 -1.7687387
A_33_P3414202 0.4194793
A_33_P3316686 -0.050790872
A_33_P3300975 0.13343638
A_33_P3263061 -0.003696511
A_33_P3261373 -0.60145473

Total number of rows: 50739

Table truncated, full table size 1235 Kbytes.




Supplementary file Size Download File type/resource
GSM1841146_NF-C_3.txt.gz 21.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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