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Sample GSM1168490 Query DataSets for GSM1168490
Status Public on Aug 21, 2013
Title T4_pitM
Sample type RNA
 
Source name maternal exposure to dioxin, pitM
Organism Rattus norvegicus
Characteristics strain: Wistar
agent (mother exposed to): TCDD
gender (pup): male
age (pup): PND70
tissue (pup): pituitary
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 5
replicate 2
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

Data table header descriptions
ID_REF
VALUE quantile normalized signal (non-log scaled) and Detection P-value.
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1348778 602.275749 0
ILMN_1348782 747.8401498 0
ILMN_1348783 196.1643047 0.01091
ILMN_1348784 170.1743744 0.12121
ILMN_1348786 210.7931967 0.00848
ILMN_1348787 130.1959381 0.99758
ILMN_1348789 143.0900453 0.77091
ILMN_1348790 246.1329943 0.00364
ILMN_1348791 156.7296643 0.3103
ILMN_1348792 142.0968422 0.82182
ILMN_1348793 160.7280745 0.25455
ILMN_1348794 132.917897 0.99273
ILMN_1348795 149.3347628 0.52364
ILMN_1348797 146.9991285 0.61333
ILMN_1348798 141.0336661 0.86061
ILMN_1348799 500.3627198 0
ILMN_1348800 213.4293922 0.00727
ILMN_1348802 141.3902323 0.8497
ILMN_1348804 240.3113039 0.00485
ILMN_1348806 160.5129189 0.25818

Total number of rows: 22523

Table truncated, full table size 689 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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