|
| Status |
Public on Jun 25, 2015 |
| Title |
day4_irradiated_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
C57BL/6, irradiated, day 4, rep1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole blood
strain: C57BL/6
|
| Treatment protocol |
C57BL/6 mice (approximately 10-12 weeks old, 25-30 g) were received from Charles River Laboratories (Frederick, MD) and were quarantined for 14 days prior to group assignment by body weight stratification for randomization into the study. Animals were administered 90-Strontium intravenously by tail vein injection with 200 ± 0.3 kBq 85/90SrCl2 solution in a volume of 0.05 mL
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All blood samples were collected by cardiac puncture in a sterile hood. For each animal ~0.4 mL of blood was collected into 2 mL of PAXgene Blood RNA stabilization and lysis solution (PreAnalytix GmBH, catalog#762165), mixed thoroughly and shipped at 4ºC in temperature-stabilized containers. They were stored for a further 24 hour at 4ºC, and then incubated at room temperature for a minimum of 2 hours before proceeding with RNA isolation. RNA was purified following the PAXgene Blood RNA kit recommended protocol with on-column DNaseI treatment.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared with the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND1000 Spectrophotometer
|
| |
|
| Hybridization protocol |
1.6 microgram of cRNA, >9 pmol Cy3 per microgram cRNA was fragmented and hybridized (17 hours with rotation at 65°C) to Agilent Whole Mouse Genome Microarrays 4X44K v2 (G4846A), and then washed using the Gene Expression Hybridization Kit and GE Wash Buffers as recommended by Agilent
|
| Scan protocol |
Slides were scanned with the Agilent DNA Microarray Scanner (G2505B), and the images were analyzed (Agilent Feature Extraction Software ver. 10.7) with default parameters for background correction and flagging non-uniform features.
|
| Description |
Gene expression in mouse whole blood at day 4
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jan 08, 2015 |
| Last update date |
Jun 26, 2015 |
| Contact name |
Shanaz Adi Ghandhi |
| E-mail(s) |
[email protected]
|
| Phone |
212-3053911
|
| Organization name |
Columbia University Medical Center
|
| Department |
Center for Radiological Research
|
| Lab |
VC11-237
|
| Street address |
630, W 168th street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE64775 |
Effect of 90Sr internal emitter on gene expression in mouse blood |
|
