|
| Status |
Public on Oct 12, 2018 |
| Title |
MammaryTu_negCD_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
Mammary gland tumor, maternal control diet
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain/background: Sprague-Dawley
tissue: Mammary gland tumor
Sex: Female
age: 110 days
dam diet: Control
|
| Treatment protocol |
Pregnant Sprague-Dawley (SD) rats received control diet (CD) or Western-style diet (WD) from gestational days (GD) 12-20 and post-natal days (PND) 1-21. At weaning, the female offspring received CD until the end of the tumor bioassay. Female offspring 3 weeks old from both CD and WD groups received a single intraperitoneal dose of 50 mg/kg of N-Methyl-N-Nitrosourea (MNU) dissolved in phosphate-buffered saline acidified with acetic acid. At the end of study, the animals were euthanized and mammary tumors were removed and kept at -80°C for molecular analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the tubular/papillary mammary tumors using the miRNeasy kit (QIAGEN Inc. USA Valencia, CA - USA) according to the manufacturer’s instructions. The extracted RNA was stored at -80°C. RNA was quantified in a spectrophotometer NanoVue (GE Healthcare UK Limited, UK) and the integrity was evaluated using the equipment Agilent 2100 Bioanalyzer (Agilent Technologies, Inc. Life Sciences and Chemical Analysis Group, Santa Clara, CA, USA) under standard conditions.
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA were hybridized onto whole rat genome 4x44K oligo microarrays (G4131F, Agilent Technologies) using one color (Cy3) Low input Quick Amp labeling kit (Agilent Technologies, Inc. Life Sciences and Chemical Analysis Group, Santa Clara, CA, USA), according to manufacturer instructions. Briefly, total RNA plus spike-in controls were reverse transcribed into double-stranded cDNA. The primers used for this reaction contained consecutive thymine bases attached to a T7 promoter that paired at the 5' end of the first strand of cDNAs. Next, the T7 polymerase was added along with nucleotides labeled with fluorescent Cyanine-3 (Cy3) dye, which amplified the anti-sense complementary RNAs (cRNA).
|
| |
|
| Hybridization protocol |
1.65 ug of labeled cRNA was hybridized to microarray slides (Whole rat genome-4X44K oligo microarrays-G4112F, Agilent Technologies) at 65°C for 17 hours. Slides were then washed and scanned following Agilent's recommendations.
|
| Scan protocol |
The hybridization signals were captured using the Agilent G4900DA SureScan Microarray Scanner System (Agilent Technologies, Inc. Life Sciences and Chemical Analysis Group, Santa Clara, CA, USA).
|
| Description |
251487921671 - GE1_1105_Oct12_1_2 s9
Gene expression array of mammary gland tumor in post-natal day 110.
Mammary gland tumor, negative control, replicate 4.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software v.15.5 using the default protocol (GE1_1105_Oct12 and Grid:014879_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Mar 12, 2017 |
| Last update date |
Oct 12, 2018 |
| Contact name |
Lucas Tadeu Bidinotto |
| E-mail(s) |
[email protected]
|
| Organization name |
Barretos Cancer Hospital
|
| Lab |
Molecular Oncology Research Center
|
| Street address |
Antenor Duarte Vilela, 1331
|
| City |
Barretos |
| State/province |
SP |
| ZIP/Postal code |
14784-400 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL4135 |
| Series (1) |
| GSE96520 |
Maternal Western-style diet alters the transcriptome of chemically induced mammary tumors in female offspring rats |
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