|
| Status |
Public on May 05, 2018 |
| Title |
Pio_16mgkg_F_90d_2 [miRNA] |
| Sample type |
RNA |
| |
|
| Source name |
bladder, female, Pioglitazone, 16 mg/kg/day, 90 days
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: bladder urothelium
strain: Sprague-Dawley
Sex: female
treatment_agent: Pioglitazone
treatment_dosage: 16 mg/kg/day
treatment_timepoint: 90 days
group: Pio_16mgkg_F_90d
corresponding_control: Control_F_90d
qc_okay: yes
|
| Treatment protocol |
The rats received a daily oral administration of 10 mL/kg body weight of vehicle or test compound solution for either 3, 28 or 90 days. One day after the last treatment, the animals were anaesthetised in isoflurane, exsanguinated from the abdominal aorta and subjected to necropsy. The bladder was rapidly isolated and cut longitudinally into halves. The urothelium was scraped off with a scalpel and snap frozen in liquid nitrogen.
|
| Growth protocol |
Sprague-Dawley rats (10/sex/group) were treated orally with vehicle (0.5% methylcellulose 15), Pioglitazone hydrochloride (CAS No 112529-15-4) at 16 or 63 mg/kg/day, or Rosiglitazone maleate (CAS 155141-29-0) at 10 mg/kg/day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Qiagen RNeasy kit following the manufacturer's recommendations. For extraction, the filter paper was trimmed, and transferred to the lysis buffer. All handling was done on dry ice.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled miRNA was prepared from 0.1 ug RNA using the microRNA complete Labelling and Hybridisation Kit (Agilent) according to the manufacturer's instructions, followed by purification with Micro Bio Gel Filtration Columns (Bio-Rad) concentration using a Speed-Vac, 45°C 30 minutes.
|
| |
|
| Hybridization protocol |
Entire Cy3-labelled miRNA was fragmented at 100°C for 5 minutes in a reaction volume of 45ul containing 10x Agilent blocking agent and 2x Agilent hybridization buffer following the manufacturers instructions. On completion of the fragmentation reactionsamples were hybridized to Agilent Rat miRNA Microarrays (G4473B) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G25056) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
Raw data was RMA normalized using the limma package for R/Bioconductor.
|
| |
|
| Submission date |
May 06, 2015 |
| Last update date |
May 05, 2018 |
| Contact name |
Jonathan Moggs |
| E-mail(s) |
[email protected]
|
| Organization name |
Novartis
|
| Street address |
Fabrikstrasse 2
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL14860 |
| Series (2) |
| GSE68387 |
IMI MARCAR Project: towards novel biomarkers for cancer risk assessment |
| GSE68604 |
Trancriptional profiling of rat bladder after daily administration of Pioglitazone and Rosiglitazone in vivo (miRNA) |
|
