|
| Status |
Public on Nov 14, 2018 |
| Title |
0Gy4h_#2 |
| Sample type |
RNA |
| |
|
| Source name |
Small intestine_4hr_0Gy
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/cA Jcl
gender: female
age: 8w
pre-treated with: saline
tissue: small intestine
|
| Treatment protocol |
BALB/cA Jcl mice were irradiated with C-ion after intraperitnial administration of saline or FGF1 or FGF1/CPP-C. Four hours later, small intestine was sampled and immediately frozen using liquid nitrogen, and then stored at -80 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Trizol reagent (Life Technologies, Carlsbad, CA) and RNeasy mini 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 Low Input Quick Amp Labeling Kit (one-color) (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 |
1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Ver 2.0, 4x44K (G2519F) for 17 hours at 65°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°C GE Wash buffer 2 (Agilent), then dried.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
180314_#5
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (Protocol: GE1-v1_95_Feb07 and Grid: 026655_D_F_20150604) to obtain background subtracted and spatially determined Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
Nov 14, 2018 |
| Contact name |
Atsuko Ishikawa |
| Organization name |
National Institute of Radiologocal Sciences
|
| Department |
Research Center for Charged Particle Therapy
|
| Lab |
RadGenomics Project
|
| Street address |
Anagawa 4-9-1
|
| City |
Chiba |
| State/province |
Chiba |
| ZIP/Postal code |
2638555 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10333 |
| Series (1) |
| GSE113641 |
The FGF1/CPP-C chimera protein protects against intestinal adverse effects of Carbon-ion radiotherapy without exacerbating pancreatic carcinoma. |
|
