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| Status |
Public on Apr 29, 2019 |
| Title |
SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 5 |
| Sample type |
SRA |
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| Source name |
Contusion SCI + Large Cage
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| Organism |
Rattus norvegicus |
| Characteristics |
Sex: female
strain: Sprague-Dawley
tissue: liver
injury type: Contusion SCI
age at injury: 8-9 weeks (weight-based estimate)
days after injury: 11.5 weeks post injury
sci level: Level T2
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| Treatment protocol |
All rats were initially gentled for two weeks. Animals were anaesthetized with pentobarbital (50 mg/kg, IP) and given prophylactic antibiotics (gentamicin sulphate, 15 mg/kg, SC) prior to surgery and again 3 and 5 days post-injury. For animals in the contusion injury groups, a single level laminectomy was performed at the T2 vertebrae before receiving a moderately-severe contusion injury (25 g-cm SCI) at the T2 spinal cord level using the NYU Impactor. For animals in the transection injury group, a single level laminectomy was performed at the T2 vertebrae before receiving a complete transection of the spinal cord at T2. All injured animals received buprenorphine (0.1 mg/kg, SC) twice a day for three days. Manual bladder expression was performed twice daily for each animal until reflexive voiding returned. After recovery, animals in the SCI Cage Size groups were housed two/cage in standard cages (22” x 12.5” x 8”), tiny cages (7.5” x 8.5” x 8”), to restrict their movement, or large cages (16” x 20” x 8” ), to allow for greater movement for the duration of the study. The subjects were randomized into three groups: No SCI+Standard, CONT SCI+Tiny, and CONT SCI+Large. For animals in the SCI+Activity groups, this involved housing animals two/cage in standard cages (22” x 12.5” x 8”) or tiny cages (7.5” x 8.5” x 8”, to restrict their activity) for the duration of the study. The subjects were randomized into five groups: No SCI, TX SCI, CONT SCI, CONT SCI + swimming (SWIM), and CONT SCI + shallow water walking (SWW). Swimming and shallow water walking (three five minute bouts separated by a short break twice/day) began 10 days post-injury and was conducted 5 consecutive days/week for 8 weeks. These 15 minutes sessions were separated with an hour break in between.
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| Growth protocol |
All animal procedures were performed in accordance with the Public Health Service Policy on Humane Care and Use of Laboratory Animals (Institute of Laboratory Animal Resources, National Research Council, 1996) and the University of Louisville Institutional Animal Care and Use Committee. Female Sprague Dawley rats of body weight 235-249 g were obtained from Sprague Dawley, Inc. (Indianapolis, IN). All rats were housed in standard cages and subjected to a 12h-light/dark cycle. Tap water and a standard rodent diet were available to all rats ad libitum.
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| Extracted molecule |
polyA RNA |
| Extraction 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1. Quality trimming was not deemed necessary.
The sequences were directly aligned to the Rattus norvegicus reference genome assembly (Rn6) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq using Ensembl annotations (Rn6 version 93).
The annotation file was parsed to exclude mitochondria genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 24,613 gene locations.
Genome_build: rn6
Supplementary_files_format_and_content: Expression data tracks in UCSC Genome Browser bigwig format were generated for each sample. GeneMatrix_RawCounts_ALL.txt includes gene counts for all samples and is available on the series record.
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| Submission date |
Jan 08, 2019 |
| Last update date |
Apr 29, 2019 |
| 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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| Platform ID |
GPL20084 |
| Series (2) |
| GSE124819 |
Activity-induced changes in the liver transcriptome after chronic spinal cord injury |
| GSE129704 |
Spinal cord injury |
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| Relations |
| BioSample |
SAMN10714738 |
| SRA |
SRX5227278 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3554487_SW_05_29_T2_LargeCage_5-106800699_NORM.bw |
602.1 Mb |
(ftp)(http) |
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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