Gene Expression Profiling in Spinal Cord Injury

Affymetrix Rat Neuro U34 Chip Time Course

Carmel et al., Physiological Genomics.  Download formatted Acrobat version (~1 Mb). 
Visit  Physiological Genomics.

Rats were contused using the MASCIS impactor at a moderate setting (10.0 g dropped 25.0 mm).  At various times following injury, a 5 mm segment of spinal cord centered at the site of injury (the "injury" or I segment)  was excised and frozen for RNA preparation.  Additionally, a 5 mm segment just distal to the I segment was collected and named "D1."  Biotinylated aRNA probes were prepared following procedures provided by Affymetrix.  Probes were hybridized with the Affymetrix Rat Neuro U34 chip, containing approximately 1,200 probes sets (each set containing 16-20 pairs of wild-type and point-mutated 25-mer oligo probes).  Hybridization, scanning and preliminary analysis was performed at the Center for Applied Genomics of the International Center for Public Health, Newark, NJ.  

All microarray hybridizations were performed in triplicate.  Results from each array were scaled to make the mean Average Difference equal to 2,500, excluding the upper and lower two percentile.  Mean average differences were calculated only when Affymetrix software called a consensus "present" call in all three arrays.  For Fold-Change calculations, three array results from each time point were compared with uninjured controls ("0 hrs"), producing 9 binary comparisons.  Mean Fold-Change values were calculated only when an 80% consensus was reach on the Affymetrix increase or decrease call.  Results were clustered using the Stanford Cluster software (for Hierarchical clustering) and the MIT/Whitehead GeneCluster software (for self-organizing maps).

Animals pooled for target preparation: I Segment and D1 Segment

Clustered gene images:  I Segment | D1 Segment

Download entire raw database: I Segment | D1 Segment (Warning--8.8 Mb each--Very large download!!)

Link to newer data from Alan Faden's lab [Datasets available]

Search Array Results

I Segment (5 mm centered at impact site)

Gene Name/Keyword/Accession:

Search Self-Organized Maps


Gene Name/Keyword/Accession:

D1 Segment (5 mm segment distal of I segment)

Gene Name/Keyword/Accession:



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