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Series GSE62760 Query DataSets for GSE62760
Status Public on Oct 26, 2015
Title T Cell Deficiency in Spinal Cord Injury: Altered Locomotor Recovery and Whole-Genome Transcriptional Analysis
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary T cells undergo autoimmunization following spinal cord injury (SCI) and play both protective and destructive roles during the recovery process. T-cell deficient athymic nude (AN) rats recover better than immunocompetent Sprague-Dawley (SD) rats following spinal cord transection. In the present study, we evaluated locomotor recovery in SD and AN rats following moderate spinal cord contusion. To explain variable locomotor outcome, we assessed whole-genome expression using RNA sequencing, in the acute (1 week post-injury) and chronic (8 weeks post-injury) phases of recovery. AN rats demonstrated greater locomotor function than SD rats only at 1 week post-injury, coinciding with peak T cell infiltration in immunocompetent rats. Genetic markers for T cells and helper T cells were acutely enriched in SD rats, while AN rats expressed genes for Th2 cells, cytotoxic T cells, NK cells, mast cells, IL-1a, and IL-6 at higher levels. Acute enrichment of cell death-related genes suggested that SD rats undergo secondary tissue damage from T cells. Additionally, SD rats exhibited increased acute expression of voltage-gated potassium (Kv) channel-related genes. However, AN rats demonstrated greater chronic expression of cell death-associated genes and less expression of axon-related genes. We put forth a model in which T cells facilitate early tissue damage, demyelination, and Kv channel dysregulation in SD rats following contusion SCI. However, compensatory features of the immune response in AN rats cause delayed tissue death and limit long-term recovery. T cell inhibition combined with other neuroprotective treatment may thus be a promising therapeutic avenue.
Overall design 2x2 model with 4 groups and 12 total samples. 2 rat strains (athymic nude [AN] and Sprague-Dawley [SD]) and 2 time points (1 week post-injury [acute] and 8 weeks post-injury [chronic]). 3 samples per group, for a total of 12 samples. No technical replicates were performed. Acute SD group = rats 618, 619, and 620. Chronic SD group = rats 605, 606, and 608. Acute AN group = rats 714, 715, and 717. Chronic AN group = rats 707, 712, and 713.
Contributor(s) Satzer D, Miller C, Maxon J, Voth J, DiBartolomeo C, Mahoney R, Dutton JR, Low WC, Parr AM
Citation(s) 26546062
Submission date Oct 28, 2014
Last update date May 15, 2019
Contact name Ann Margaret Parr
Organization name University of Minnesota
Department Department of Neurosurgery
Lab MTRF 4-401
Street address 2001 6th St SE
City Minneapolis
State/province MN
ZIP/Postal code 55455
Country USA
Platforms (1)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (12)
GSM1532989 Rat 618
GSM1532990 Rat 619
GSM1532991 Rat 620
BioProject PRJNA265064
SRA SRP049326

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Supplementary file Size Download File type/resource
GSE62760_Acute_Cuffdiff_DGE.txt.gz 671.4 Kb (ftp)(http) TXT
GSE62760_Chronic_Cuffdiff_DGE.txt.gz 672.3 Kb (ftp)(http) TXT
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