|
| Status |
Public on Jan 01, 2008 |
| Title |
500 nM BPDE, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
human amnion epithelial FL cells exposed to 500 nM BPDE for 2 h, and subsequently recovered for additional 4 h
|
| Organism |
Homo sapiens |
| Characteristics |
Strain: human amnion epithelial FL cells, Gender: female
|
| Treatment protocol |
At the logarithmic growth phase, the cultures were exposed to vehicle control (0.1%, V/V) and increasing doses (5, 50, 500 nM) of anti-BPDE for 2 h in a culture medium that did not contain 10% newborn bovine serum, followed by additional growth for 4 h in a fresh medium containing 10% newborn bovine serum. The cultures were rinsed twice with Hank’s buffer before each change of the medium.
|
| Growth protocol |
Human amnion epithelial FL cells were grown as monolayers in minimal essential medium (MEM, Gibco-Invitrogen, Carlsbad, CA) supplemented with 10% newborn bovine serum (Gibco-Invitrogen), 100 U/mL penicillin, and 100 µg/mL streptomycin in a humidified atmosphere of 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Trizol reagents (Invitrogen), and further purified using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturers’ protocols. Isolated total RNA was analyzed on an Agilent Bioanalyzer 2100 to verify that the starting material was of good quality.
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)
|
| |
|
| Hybridization protocol |
The biotinlyated cRNAs were fragmented and hybridized to the microarrays at 45°C for 16 h in the Hybridization Oven 640 rotating at 60 rpm. Following hybridization, the microarrays were washed and stained with streptavidin-phycoerythrin in the Fluidics Station 400,
|
| Scan protocol |
Based on the Affymetrix Microarray Suite 5.0 platform, GeneChips were scanned using the GeneChip Scanner 3000, and original Affymetrix .dat proprietary output files were generated.
|
| Description |
Gene expression data from FL cells exposed to 500 nM BPDE
|
| Data processing |
Affymetrix MAS5.0 was used to obtain gene expression signals and normalization of our arrays’ signals by global scaling to the target of 500 for U133A and U133B for each array. Detection call and change call were generated through single array analysis and two-array comparison analysis, respectively. A probe set was delimited as differentially expressed only if it showed at least one “Present” detection call and exhibited the consistent “Increase” or “Decrease” change calls in the orthogonal comparisons of the two BPDE and two control treatment microarrays.
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| |
|
| Submission date |
May 01, 2007 |
| Last update date |
May 01, 2007 |
| Contact name |
Lu XiangYun |
| E-mail(s) |
present81@163.com
|
| Organization name |
Zhejiang University School of Medicine
|
| Street address |
388 Yuhangtang Road
|
| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL97 |
| Series (1) |
| GSE7675 |
Early transcriptional responses induced by benzo(a)pyrene diol epoxide in human amnion epithelial FL cells |
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