|
| Status |
Public on Feb 28, 2012 |
| Title |
Normal_DRG_RL4-5 |
| Sample type |
RNA |
| |
|
| Source name |
Normal dorsal root ganglia (DRG)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6
tissue: dorsal root ganglia
|
| Treatment protocol |
Adult female C57Bl6 mice were used. Nerve crush was performed to study the mechanisms of nerve repair. Nerve transection was performed to differentiate the distal (degenerating) and proximal (regenerating) events of nerve injury. Animals were anesthetized with 4% isofluorane (Aearrane; Baxter, IL) in 55% Oxygen and the sciatic nerves were exposed unilaterally at the mid-thigh level. Nerves were transected using surgical scissors or crushed using fine, smooth-surface forceps twice for 5 sec each in rats or once for 3 sec in mice. Sham-operated control includes the sciatic nerve exposure without otherwise any manipulation. Animals were sacrificed by an i.p. injection of rodent anesthesia cocktail containing Nembutal (50 mg/ml, Ovation Pharmaceuticals, IL) and Diazepam (5 mg/ml, Hospira inc., Lake Forest, IL) in 0.9% saline (Steris Labs, Phoenix, AZ), followed by lethal i.p. injection of Beuthanasia (100-150 mg/ml, Schering-Plough Animal Health, Canada). The sciatic nerve and lumbar (L) 4 and 5 dorsal root ganglia (DRG) ipsilateral and contralateral to injury were isolated for analyses. Animals were handled in accordance with the NIH Guide for the Care and Use of Laboratory Animals and the protocols approved by the VA San Diego Institutional Animal Care and Use Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from nerves and DRG using TRIzol reagent and purified using the RNeasy columns (Qiagen). The RNA purity was estimated by measuring the OD260/280 and the 260/230 ratios. The integrity of the RNA samples was validated using an Experion automated electrophoresis system (Bio-Rad).
|
| Label |
Cy3
|
| Label protocol |
Samples of total RNA (500 ng) were labeled using an Illumina RNA Amplification Kit (Ambion).
|
| |
|
| Hybridization protocol |
The obtained labeled copy RNA samples (1,500 ng) were hybridized 18 h at 58°C to a MouseRef-8 v2.0 Expression BeadChip (Illumina) according to the manufacturer's instructions. BeadChips were then washed and developed using fluorolink streptavidin-Cy3 (GE Healthcare).
|
| Scan protocol |
BeadChips were scanned using an Illumina BeadArray Reader.
|
| Description |
pool of 6 animals; 5125380031_D
|
| Data processing |
The raw data were processed using Feature Extraction software version 10.5. The initial analysis and normalization to the median were performed using GeneSpring GX software (Agilent). Differentially expressed mRNAs with signal intensities higher than two-fold over the background standard deviation were filtered by t-test with p<0.05. Only the statistically significant data (p<0.05) were used to calculate gene expression ratios in the samples.
|
| |
|
| Submission date |
Nov 03, 2011 |
| Last update date |
Feb 28, 2012 |
| Contact name |
Andrei Chernov |
| E-mail(s) |
achernov@ucsd.edu
|
| Phone |
858 952 2854
|
| Organization name |
University of California San Diego
|
| Department |
Anesthesiology
|
| Lab |
Chernov Lab
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE33454 |
Matrix metalloproteinase-9 and TIMP-1 in peripheral nerve: Implications for myelin formation |
|
