|
| Status |
Public on Sep 27, 2016 |
| Title |
Renal cortex, VC, Gavage, replicate 2 (B114) |
| Sample type |
RNA |
| |
|
| Source name |
Renal cortex, VC, Gavage
|
| Organism |
Rattus norvegicus |
| Characteristics |
treatment: water
strain: Sprague-Dawley
gender: male
administration: Gavage
tissue: renal cortex
|
| Treatment protocol |
Three animals were administrated water for four weeks, the other three animals were administrated cisplatin (3.75 mg/kg/day) for four weeks.
|
| Growth protocol |
Five week-old male Sprague-Dawley (Crl:CD(SD)) Rat were purchased from Charles River Japan. They were housed in an air-conditioned room at 21 to 25 deg C and 40 to 70% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (Oriental Yeast Co.), with tap water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the miRNA Neasy kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60 deg C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Rat GE 8x60K Microarray Toxplus for 17 hours at 65 deg C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 deg C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.
|
| Description |
B114_28_Kc_VC2
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 045522_D_F_20130222) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
Sep 27, 2016 |
| Contact name |
Hiroshi Matsumoto |
| E-mail(s) |
[email protected]
|
| Organization name |
Chemicals Evaluation and Research Institute, Japan
|
| Street address |
1600 Shimotakano, Sugito-machi
|
| City |
Kitakatsushika-gun |
| State/province |
Saitama |
| ZIP/Postal code |
345-0043 |
| Country |
Japan |
| |
|
| Platform ID |
GPL22435 |
| Series (2) |
| GSE87272 |
Gene expression changes of cisplatin-induced in renal cortex of rats |
| GSE87288 |
Gene expression changes chemically-induced in renal cortex of rats |
|
