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Sample GSM1841152 Query DataSets for GSM1841152
Status Public on Aug 01, 2015
Title iodine-biofortified lettuce 3
Sample type RNA
 
Channel 1
Source name Caco-2 colorectal adenocarcinoma cells, iodine-biofortified lettuce, 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 iodine-biofortified lettuce
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 -0.38545322
DarkCorner -0.13952327
A_23_P117082 -0.18233493
A_33_P3246448 -0.3600678
A_33_P3318220 -0.36075735
A_33_P3236322 0.0766323
A_33_P3319925 -0.27088588
A_21_P0000509 1.3844692
A_21_P0000744 0.17477606
A_24_P215804 -0.011768486
A_23_P110167 -0.025398197
A_33_P3211513 0.33520168
A_23_P103349 0.9062583
A_32_P61480 -0.3826581
A_33_P3788124 -0.3664003
A_33_P3414202 0.17176534
A_33_P3316686 -0.05175211
A_33_P3300975 0.28085896
A_33_P3263061 0.076860435
A_33_P3261373 -1.0066863

Total number of rows: 50739

Table truncated, full table size 1237 Kbytes.




Supplementary file Size Download File type/resource
GSM1841152_I-L_3.txt.gz 21.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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