|
| Status |
Public on Aug 21, 2013 |
| Title |
C4_HypM |
| Sample type |
RNA |
| |
|
| Source name |
maternal exposure to vehicle, HypM
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
agent (mother exposed to): vehicle
gender (pup): male
age (pup): PND70
tissue (pup): hypothalamus
|
| Treatment protocol |
Pregnant Wistar rats were orally treated with TCDD (1 mg/kg in corn oil) at GD15.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted from the pituitary and hypothalamus of PND70 male pups according to the manufacturer's protocol (RNeasy Mini Kits).
|
| Label |
biotin
|
| Label protocol |
The total RNA (250 ng) was converted to its biotinylated-cRNA according to the manufacturer’s procedures (Illumina TotalPrep RNA Amplification Kit). Briefly, reverse transcription to synthesize the first-strand cDNA was performed for 2 hours at 42°C, using an oligo (dT) primer bearing a T7 promoter and reverse transcriptase (ArrayScript; Ambion). The second strand cDNA was synthesized by incubating the first strand for 2 hours at 16°C in the presence of DNA polymerase I and ribonuclease H. After cDNA purification by a short column, the eluted cDNA was used for in vitro transcription with T7 RNA polymerase. In vitro transcription was performed at 37°C for 14 hours, yielding the multiple copies of the biotinylated antisense RNA originated from respective mRNAs in the sample.
|
| |
|
| Hybridization protocol |
The biotinylated-cRNA (total amount, 1,500 ng) prepared from each sample was overlaid onto an individual array spot of the rat microarray chip (RatRef12-v1 BeadChip; Illumina), according to the hybridization protocol. The chip was hybridized at 58°C for 19 hours.
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
SAMPLE 9
replicate 3
|
| Data processing |
The data were normalized by quantile normalization using lumi and preprocess package in R. This series includes two dataset; hypothalamic and pituitary samples (each case; N=3x2). The normalization applied each dataset.
|
| |
|
| Submission date |
Jun 19, 2013 |
| Last update date |
Aug 21, 2013 |
| Contact name |
Tomoki Takeda |
| E-mail(s) |
takeda@phar.kyushu-u.ac.jp
|
| Phone |
+81-92-642-6587
|
| Fax |
+81-92-642-6588
|
| Organization name |
Kyushu University
|
| Department |
Pharmaceutical sciences
|
| Lab |
Molecular life sciences
|
| Street address |
3-1-1 Maidashi, Higashi-ku
|
| City |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6101 |
| Series (1) |
| GSE48100 |
Effect of maternal exposure to dioxin on the pituitary and hypothalamic expression of genes in PND70 male pups |
|
