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Sample GSM174819 Query DataSets for GSM174819
Status Public on Jun 01, 2007
Title Quercetin day 05 sample 1
Sample type RNA
 
Source name Human colon cancer cell line Caco-2
Organism Homo sapiens
Characteristics The Caco-2 cell line is derived from a male Caucasian with a colon tumor
Biomaterial provider American Type Culture Collection (ATCC)
Treatment protocol Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) heat inactivated mycoplasma tested fetal calf serum, 2 mM L-glutamine (6 mM final concentration), 1% (v/v) MEM non-essential amino acids and 50 µg/ml gentamicin. Quercetin in DMEM culture medium was stabilized by 1 mM ascorbate
Growth protocol Caco-2 cells of passage 37 were seeded (1 : 10 split ratio) in triplicate on polycarbonate membrane transwell® inserts (Corning Life Sciences, Cambridge, U.K.), with a membrane diameter of 75 mm (growth area 44 cm2, 0.4 µm pore size) at a density of approx. 40,000 cells/cm2. After 2 days, cell cultures reached confluency, and this time point was considered experimental day 0 and the initial exposure to quercetin. Cells were exposed for a total number of 9 days.
Extracted molecule total RNA
Extraction protocol On days 5 and 10 post-confluency, cells were first rinsed with ice cold phosphate buffered saline without calcium or magnesium (InvitrogenTM Life Technologies, Breda, The Netherlands). Subsequently, cells were harvested in 2 x 0.75 ml of ice-cold TRIzol (Life Technologies, Paisley, U.K.), immediately frozen in liquid nitrogen and stored at -80°C for up to 2 months, until RNA isolation according to the TRIzol protocol. Following isolation, total RNA was purified with RNeasy Midi columns (QIAGEN, Westburg, Leusden, The Netherlands), including a DNAse incubation step. Quality of purified total RNA was determined on a UV-VIS spectrofotometer (Shimadzu Benelux, ‘s Hertogenbosch, The Netherlands) by calculation of the A260/A280 ratio (1.7 - 2.0) and confirmed on a Lab-on-a-Chip on the Agilent 2100 bioanalyser (Agilent Technologies, Palo Alto, California, U.S.A.) by determining the 28S/18S ribosomal RNA ratio
Label Biotin
Label protocol Labeling protocol according to Affymetrix® GeneChip® Expression Analysis Technical Manual
 
Hybridization protocol Hybridization protocol according to Affymetrix® GeneChip® Expression Analysis Technical Manual
Scan protocol Scan protocol with GeneChip® Scanner 3000 7G, according to Affymetrix® GeneChip® Expression Analysis Technical Manual
Description Probe sets with an “absent call” (P ≥ 0.065 for HG-U133A 2.0 GeneChip® arrays) across all 8 arrays (n = 7,285) were considered not to be affected by quercetin treatment and/or incubation time and were therefore excluded from further analyses.
Data processing CEL files were imported in Rosetta Resolver 5.0 (Rosetta Inpharmatics LLC, Seattle, U.S.A.), applying data pre-processing (to estimate and reduce systematic errors) and error modeling (for improvement of accuracy of the present and absent calls for low replicate numbers).
 
Submission date Mar 13, 2007
Last update date Apr 27, 2007
Contact name Ashwin Dihal
E-mail(s) [email protected]
Phone +31 (0)30-6944545
Fax +31 (0)30 6944989
Organization name TNO Quality of Life
Department Business Unit Physiologival Sciences
Street address Utrechtseweg 48
City Zeist
ZIP/Postal code 3704 HE
Country Netherlands
 
Platform ID GPL571
Series (1)
GSE7259 Pathway and single gene analysis of Caco-2 cell differentiation by ascorbate-stabilized quercetin

Data table header descriptions
ID_REF
VALUE Probeset intensity
ABS_CALL Absent or Present call
DETECTION P-VALUE P-value for Absent or Present call (Present call: P<0.065)

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 167.132 P 0.000169227
AFFX-BioB-M_at 271.85 P 6.02111e-05
AFFX-BioB-3_at 163.371 P 7.00668e-05
AFFX-BioC-5_at 352.305 P 6.02111e-05
AFFX-BioC-3_at 431.113 P 6.02111e-05
AFFX-BioDn-5_at 642.55 P 4.42873e-05
AFFX-BioDn-3_at 2378.29 P 4.42873e-05
AFFX-CreX-5_at 4515.02 P 4.42873e-05
AFFX-CreX-3_at 6876.08 P 4.42873e-05
AFFX-DapX-5_at 156.376 P 7.00668e-05
AFFX-DapX-M_at 283.499 P 0.000856509
AFFX-DapX-3_at 350.023 P 8.14279e-05
AFFX-LysX-5_at 20.7781 P 0.023919
AFFX-LysX-M_at 24.1327 M 0.0501994
AFFX-LysX-3_at 47.8834 P 0.000296708
AFFX-PheX-5_at 41.9698 P 5.16732e-05
AFFX-PheX-M_at 53.9414 P 0.000662269
AFFX-PheX-3_at 51.9876 P 0.000389797
AFFX-ThrX-5_at 41.0143 P 0.000340305
AFFX-ThrX-M_at 64.0348 P 5.16732e-05

Total number of rows: 22277

Table truncated, full table size 678 Kbytes.




Supplementary file Size Download File type/resource
GSM174819.CEL.gz 1.7 Mb (ftp)(http) CEL
GSM174819.CHP.gz 125.3 Kb (ftp)(http) CHP
Processed data provided as supplementary file

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