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Series GSE56842 Query DataSets for GSE56842
Status Public on Apr 17, 2015
Title Identification of axonal regeneration-associated genes after spinal cord injury in adult zebrafish
Organism Danio rerio
Experiment type Expression profiling by array
Summary Adult zebrafish regenerate about half of cerebrospinal axons by six weeks after a complete spinal cord transection. We isolated the two populations of neurons that successfully regenerated their axons versus those that did not and isolated the total RNA. Cerebrospinal neurons from unlesioned animals were also collected to serve as controls. Whole transcriptome microarray was performed to determine axonal regeneration-associated genes. For each condition (regenerated, non-regenerated and control neurons) we had 3 biological replicates that consisted of neurons pooled from 3 to 9 zebrafish.
 
Overall design A complete spinal cord transection with Fluororuby retrograde tracing was performed at the 8th vertebra level in adult zebrafish. Fluororuby labeled all the neurons in the brain that project their axons to the 8th vertebra. Three weeks later Fluoroemerald was injected 4mm distally from the spinal cord transection site, thereby labeling all neurons that regenerated their axons to this level. The zebrafish were sacrificed 1 week after Fluoroemerald tracing, brain enzymatically dissociated and cells sorted using fluorescence-activated cell sorter. After sorting the total RNA was extracted, amplified and labeled with biotin and then hybridized to Affymetrix 3' IVT gene expression microarray. Unlesioned fish were traced with Fluororuby at the 8th vertebra level and labeled neurons isolated 1 week after to serve as control for gene expression microarray.
 
Contributor(s) Vajn K, Milosevic J, Tapanes-Castillo A, Plunkett JA, Oudega M
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Submission date Apr 16, 2014
Last update date Jan 25, 2018
Contact name Katarina Vajn
E-mail(s) kav31@pitt.edu
Phone 4126483270
Organization name University of Pittsburgh
Street address 200 Lothrop St
City Pitsburgh
State/province PA
ZIP/Postal code 15213
Country USA
 
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (9)
GSM1370120 zebrafish neurons control, biological rep 1
GSM1370121 zebrafish neurons control, biological rep 2
GSM1370122 zebrafish neurons control, biological rep 3
Relations
BioProject PRJNA244761

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Supplementary file Size Download File type/resource
GSE56842_RAW.tar 16.3 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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