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| Status |
Public on Apr 29, 2019 |
| Title |
Activity-induced changes in the liver transcriptome after chronic spinal cord injury |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Spinal cord injury (SCI) is a devastating clinical condition resulting in significant disabilities for affected individuals. Apart from local injury within the spinal cord, SCI patients develop a myriad of complications characterized by multi-organ dysfunction. Disorders, such as lung injury, cardiovascular disease, liver damage, kidney and urinary tract dysfunction, alterations in gut microbiome, neuropathic pain, depression and altered immune responses are common in SCI patients. Such whole body, systemic responses hinder the functional recovery and can be life-threatening in SCI population. Investigations of organ specific gene expression analyses can provide a better understanding of the injury response and identify molecular targets. Consequently, this can be used to develop treatment for SCI, promoting functional recovery and overall quality of life.
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| Overall design |
The effect of post-SCI activity on the liver transcriptome was explored with two different approaches. In the first approach, liver tissue was harvested from three groups of rats housed in cages of varying size at 11.5 weeks post-SCI. The experimental groups consisted of 1) T2 contusion injury in large cages, 2) T2 contusion injury in tiny cages, and 3) uninjured controls in standard cages. In the second approach, liver tissue was harvested from five groups of rats at 11.5 weeks post SCI. Experimental groups consisted of 1) T2 contusion injury 2) T2 contusion injury followed by swimming (SWIM), 3) T2 contusion injury followed by shallow water walking (SWW), 4) T2 transection injury, and 5) uninjured contols. In the second approach, all rats were housed in tiny cages. Each experimental group consists of 4-5 replicates.
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| Contributor(s) |
Chariker JH, Ohri SS, Gomes C, Brabazon F, Harmon KA, Magnuson DS, Hetman M, Petruska JC, Whittemore SR, Rouchka EC |
| Citation(s) |
31197156, 32226812 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| P20 GM103436 |
KY IDeA Networks of Biomedical Research Excellence |
UNIVERSITY OF LOUISVILLE RESEARCH FOUNDATION |
NIGEL G.F. COOPER |
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| Submission date |
Jan 08, 2019 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
eric.rouchka@louisville.edu
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| Organization name |
University of Louisville
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| Department |
Biochemistry and Molecular Genetics
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| Lab |
KY INBRE Bioinformatics Core
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| Street address |
522 East Gray Street
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| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
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| Platforms (1) |
| GPL20084 |
Illumina NextSeq 500 (Rattus norvegicus) |
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| Samples (37)
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| GSM3554441 |
SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 1 |
| GSM3554442 |
SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 2 |
| GSM3554443 |
SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 3 |
| GSM3554444 |
SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 4 |
| GSM3554445 |
SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 5 |
| GSM3554446 |
SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 1 |
| GSM3554447 |
SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 2 |
| GSM3554448 |
SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 3 |
| GSM3554449 |
SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 4 |
| GSM3554451 |
SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 5 |
| GSM3554453 |
SCI+Exercise Group, Complete Transection + Tiny Cage, Replicate 1 |
| GSM3554454 |
SCI+Exercise Group, Complete Transection + Tiny Cage, Replicate 2 |
| GSM3554457 |
SCI+Exercise Group, Complete Transection + Tiny Cage, Replicate 3 |
| GSM3554459 |
SCI+Exercise Group, Complete Transection + Tiny Cage, Replicate 4 |
| GSM3554461 |
SCI+Exercise Group, No SCI + Tiny Cage, Replicate 1 |
| GSM3554463 |
SCI+Exercise Group, No SCI + Tiny Cage, Replicate 2 |
| GSM3554465 |
SCI+Exercise Group, No SCI + Tiny Cage, Replicate 3 |
| GSM3554467 |
SCI+Exercise Group, No SCI + Tiny Cage, Replicate 4 |
| GSM3554469 |
SCI+Exercise Group, Contusion SCI + Tiny Cage, Replicate 1 |
| GSM3554471 |
SCI+Exercise Group, Contusion SCI + Tiny Cage, Replicate 2 |
| GSM3554473 |
SCI+Exercise Group, Contusion SCI + Tiny Cage, Replicate 3 |
| GSM3554475 |
SCI+Exercise Group, Contusion SCI + Tiny Cage, Replicate 4 |
| GSM3554477 |
SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 1 |
| GSM3554479 |
SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 2 |
| GSM3554482 |
SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 3 |
| GSM3554485 |
SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 4 |
| GSM3554487 |
SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 5 |
| GSM3554489 |
SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 1 |
| GSM3554493 |
SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 2 |
| GSM3554495 |
SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 3 |
| GSM3554497 |
SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 4 |
| GSM3554499 |
SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 5 |
| GSM3554501 |
SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 1 |
| GSM3554503 |
SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 2 |
| GSM3554505 |
SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 3 |
| GSM3554507 |
SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 4 |
| GSM3554509 |
SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 5 |
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA513865 |
| SRA |
SRP176640 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE124819_GeneMatrix_RawCounts_ALL_UpdatedSampleNames_UpdatedCounts.txt.gz |
971.3 Kb |
(ftp)(http) |
TXT |
| GSE124819_RAW.tar |
23.5 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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