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Sample GSM827125 Query DataSets for GSM827125
Status Public on Feb 28, 2012
Title D1_Injured_nerve_LND1
Sample type RNA
Source name Left nerve day 1 post-injury
Organism Mus musculus
Characteristics strain: C57Bl6
tissue: sciatic nerve
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_B
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
Phone 858 952 2854
Organization name University of California San Diego
Department Anesthesiology
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

Data table header descriptions
VALUE normalization to the median
5125380031_B.Detection Pval

Data table
ID_REF VALUE 5125380031_B.Avg_NBEADS 5125380031_B.BEAD_STDERR 5125380031_B.Detection Pval
ILMN_2896528 2906.4 39 156.015 0
ILMN_2721178 618.6 51 37.537 0
ILMN_3033922 1105.9 52 52.271 0
ILMN_3092673 5596.1 56 274.668 0
ILMN_2816356 108.6 36 6.4 0.12281
ILMN_2808939 771.5 38 52.945 0
ILMN_2634564 304.5 31 33.047 0
ILMN_2737647 105.6 33 7.223 0.1792
ILMN_2734484 398.8 42 25.414 0
ILMN_2952292 178.6 52 10.843 0
ILMN_2699078 88.2 50 5.059 0.80201
ILMN_1213681 323.5 47 16.75 0
ILMN_2735413 96 48 5.457 0.5
ILMN_2735415 95.7 37 6.873 0.51003
ILMN_2891688 800.8 43 52.774 0
ILMN_2637698 2757.7 42 151.159 0
ILMN_2674228 486.5 39 37.932 0
ILMN_2601546 94.8 37 5.572 0.54762
ILMN_1230831 83.1 31 7.509 0.92732
ILMN_2848071 104.3 24 11.942 0.20927

Total number of rows: 25697

Table truncated, full table size 834 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Raw data are available on Series record

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