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Sample GSM440043 Query DataSets for GSM440043
Status Public on Aug 13, 2009
Title Ishikawa_VeryLowDose_BPA_48h_rep1
Sample type RNA
 
Source name Ishikawa cell line, BPA, 1pM, 48hr
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 pM
treatment time: 48 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.
vLow_48h_1
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 1709.38 P 0.000972149
AFFX-BioB-M_at 3073.97 P 5.16732e-05
AFFX-BioB-3_at 1228.85 P 0.00762003
AFFX-BioC-5_at 4674.51 P 0.00010954
AFFX-BioC-3_at 3788.59 P 4.42873e-05
AFFX-BioDn-5_at 5385.81 P 6.02111e-05
AFFX-BioDn-3_at 26363.8 P 7.00668e-05
AFFX-CreX-5_at 53534.7 P 5.16732e-05
AFFX-CreX-3_at 74117.9 P 4.42873e-05
AFFX-DapX-5_at 2056.54 P 0.000258358
AFFX-DapX-M_at 3311.36 P 0.000972149
AFFX-DapX-3_at 5228.88 P 7.00668e-05
AFFX-LysX-5_at 384.921 P 0.00401721
AFFX-LysX-M_at 577.908 P 0.036569
AFFX-LysX-3_at 1236.73 P 0.000146581
AFFX-PheX-5_at 441.751 P 0.0044838
AFFX-PheX-M_at 588.271 P 0.0336773
AFFX-PheX-3_at 950.106 P 0.0103167
AFFX-ThrX-5_at 555.456 P 0.000971263
AFFX-ThrX-M_at 655.377 P 0.000340305

Total number of rows: 54675

Table truncated, full table size 1633 Kbytes.




Supplementary file Size Download File type/resource
GSM440043.CEL.gz 5.1 Mb (ftp)(http) CEL
GSM440043.CHP.gz 289.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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