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Sample GSM440026 Query DataSets for GSM440026
Status Public on Aug 13, 2009
Title Ishikawa_VeryHighDose_BPA_8h_rep4
Sample type RNA
 
Source name Ishikawa cell line, BPA, 1uM, 8hr
Organism Homo sapiens
Characteristics cell line: Ishikawa
cell line derivation: 39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.
treatment: bisphenol A
dose: 1 uM
treatment time: 8 hours
Treatment protocol Cells were gently washed in warm PBS and transferred to phenol red-free DMEM/F-12 Medium (supplemented with 10% Charcoal-Stripped Fetal Bovine Serum + 1X penicillin/streptomycin) in Corning Cell Culture Cluster wells overnight and then challenged with 1pM (very low, vL), 100pM (low, L), 10nM (high, H), and 1uM (very high, vH) levels of Bisphenol A. Prior to collection, cells were washed in warm PBS, resuspended & briefly incubated in TRI-Reagent, & finally collected (in quintuplicate replicates) at each specific time point: 8 hours, 24 hours, and 48 hours.
Growth protocol Ishikawa cells were maintained and grown (to confluency or at a desired cell density between 500,000 - 1 million cells/mL) in DMEM/F-12 Medium (supplemented with 10% Fetal Bovine Serum + 1X penicillin/streptomycin) in xenoestrogen-free Corning plasticware.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRI-Reagent and protocol provided by supplier (Molecular Research Center, Cincinnati, OH). Extracted RNA was further purified using Qiagen RNEasy columns and protocol provided by supplier (QIAgen, Valencia, CA). Quadruplicate samples were advanced to target preparation and GeneChip processing.
Label biotin
Label protocol Purified RNA was converted to cDNA target using SuperScript Choice system (Invitrogen Corp, Carlsbad, CA) and cDNA was converted to biotinylated cRNA probes using the ENZO BioArray transcript labeling kit (ENZO Life Sciences, Farmingdale, NY).
 
Hybridization protocol Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Cells known to possess both estrogen and progesterone receptors.
vHigh_8h_4
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.
 
Submission date Aug 12, 2009
Last update date Aug 12, 2009
Contact name Jay Patrick Tiesman
Organization name Procter & Gamble
Department Global Biotechnology
Lab Mason Business Center
Street address PO BOX 8006
City MASON
State/province OH
ZIP/Postal code 45040-8006
Country USA
 
Platform ID GPL570
Series (1)
GSE17624 Expression data from human Ishikawa cells treated with Bisphenol A

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 1779.93 P 0.000972149
AFFX-BioB-M_at 2741.88 P 0.00010954
AFFX-BioB-3_at 1038.69 P 0.00844047
AFFX-BioC-5_at 4508.13 P 7.00668e-05
AFFX-BioC-3_at 3990.12 P 4.42873e-05
AFFX-BioDn-5_at 5115.42 P 5.16732e-05
AFFX-BioDn-3_at 27192.1 P 6.02111e-05
AFFX-CreX-5_at 51416.2 P 4.42873e-05
AFFX-CreX-3_at 74060.9 P 4.42873e-05
AFFX-DapX-5_at 1726.58 P 0.000169227
AFFX-DapX-M_at 2896.54 P 0.00110197
AFFX-DapX-3_at 4870.22 P 5.16732e-05
AFFX-LysX-5_at 388.762 P 0.0239288
AFFX-LysX-M_at 500.745 M 0.0542134
AFFX-LysX-3_at 928.472 P 0.000224668
AFFX-PheX-5_at 512.014 P 0.0032123
AFFX-PheX-M_at 496.141 P 0.0284573
AFFX-PheX-3_at 884.908 P 0.0151826
AFFX-ThrX-5_at 488.306 P 0.00401721
AFFX-ThrX-M_at 747.748 P 0.000296708

Total number of rows: 54675

Table truncated, full table size 1631 Kbytes.




Supplementary file Size Download File type/resource
GSM440026.CEL.gz 5.0 Mb (ftp)(http) CEL
GSM440026.CHP.gz 289.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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