|
| Status |
Public on Apr 29, 2010 |
| Title |
BPA-to-Ctrl_#4 [mRNA] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
BPA-exposed rat_#4
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: Female
strain: Sprague Dawley CD
agent: BPA
tissue: the fourth abdominal mammary glands
age: 50-day-old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Fluorescent cRNA probes were prepared using Agilent Low Input RNA Fluorescent Linear Amplification Kit (Agilent Technologies) in the presence of Cy3-dCTP or Cy5-dCTP (Perkin–Elmer, Wellesley, MA, USA), and then purified using RNeasy Mini Kit (Qiagen Inc)
|
| |
|
| Channel 2 |
| Source name |
Seasame oil-exposed rat_#4
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: Female
strain: Sprague Dawley CD
agent: sesame oil (control)
tissue: the fourth abdominal mammary glands
age: 50-day-old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Fluorescent cRNA probes were prepared using Agilent Low Input RNA Fluorescent Linear Amplification Kit (Agilent Technologies) in the presence of Cy3-dCTP or Cy5-dCTP (Perkin–Elmer, Wellesley, MA, USA), and then purified using RNeasy Mini Kit (Qiagen Inc)
|
| |
|
| |
| Hybridization protocol |
Eight picograms of Cy3 and Cy5 from labeled control probe and labeled BPA group probe respectively, were used to hybridize an Agilent 60-mer oligo-microarrays slide containing 22 000 features. Slides were hybridized at 60 8C for 18 h in SureHyb chambers (Agilent Technologies)
|
| Scan protocol |
The images obtained were analyzed with Feature extraction software (Agilent Technologies) to verify the quality of the hybridization by the report of the outlier data. The intensity of the spots was measured using ImaGene 5.6 software (BioDiscovery Inc., El Segundo, CA, USA)
|
| Description |
Gene expression data from rat with BPA exposure
Gene expression data from rat with sesame oil exposure
|
| Data processing |
The data from each microarray was adjusted for background noise using the normexp procedure, and normalized by fitting the lowess curve to the of log-ratios of Cy5 to Cy3 channel and the average log-intensities of the two as implemented in the limma package
|
| |
|
| Submission date |
Apr 29, 2010 |
| Last update date |
Apr 29, 2010 |
| Contact name |
Pei-Yin Hsu |
| Organization name |
OSU
|
| Street address |
BRT836, 460W 12th Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43220 |
| Country |
USA |
| |
|
| Platform ID |
GPL4135 |
| Series (1) |
| GSE21068 |
Estrogen-mediated Epigenetic Repression of Large Chromosomal Regions through DNA Looping |
|
