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SRX5227278: GSM3554487: SW_05; Rattus norvegicus; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 30.3M spots, 2.3G bases, 949.1Mb downloads

Submitted by: NCBI (GEO)
Study: Activity-induced changes in the liver transcriptome after chronic spinal cord injury
show Abstracthide Abstract
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. 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.
Sample: SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 5
SAMN10714738 • SRS4231182 • All experiments • All runs
Library:
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Animals were sacrificed at 11.5 weeks post-SCI or equivalent uninjured age with a ketamine overdose. The transection injury group was sacrificed 8.5 weeks post-SCI. Hearts were arrested in diastole with an injection of 3M KCl. Animals were perfused with PBS supplemented with 20% RNAlater (Ambion, Life Technologies, Carlsbad, CA). Liver tissue was collected and equal amounts of tissue (200 mg) were processed for RNA isolation using Trizol (Qiagen, Germantown, MD) using standard procedures. Total RNA from each sample was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen). Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) and Set B (Cat# RS-122-2102) with poly-A enrichment.
Experiment attributes:
GEO Accession: GSM3554487
Links:
Runs: 1 run, 30.3M spots, 2.3G bases, 949.1Mb
Run# of Spots# of BasesSizePublished
SRR841819730,336,8932.3G949.1Mb2019-04-29

ID:
7063324

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