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Sample GSM1532992 Query DataSets for GSM1532992
Status Public on Oct 26, 2015
Title Rat 605
Sample type SRA
 
Source name Tissue from spinal cord injury epicenter
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley (SD)
time point: Chronic (8 weeks post-injury)
Treatment protocol Age-matched adult (16-18 week old) female SD (Hsd:SD, N=15) and AN (Hsd:RH-rnu/rnu, N=15) rats (Charles River, Wilmington, MA) received moderate (200 kdyn) contusion injury using the Infinite Horizon impactor (Precision Systems, Lexington, KY). At 1 or 8 weeks after injury, animals were anesthetized with ketamine (100 mg/kg IP) and xylazine (10 mg/kg IP). Animals underwent transcardial perfusion with phosphate buffered saline (PBS), and a 1-mm spinal cord segment through the injury site was harvested and flash-frozen in liquid nitrogen.
Growth protocol [not applicable]
Extracted molecule polyA RNA
Extraction protocol A 1-mm spinal cord segment through the injury site was harvested and flash-frozen in liquid nitrogen. RNA was extracted from tissue samples using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands). RNA quantity and quality were assessed with the Aligent 2100 Bioanalyzer (Aligent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Analysis of RNA-seq data was carried out using the Galaxy software platform hosted by the Minnesota Supercomputing Institute. Reads first underwent quality control assessment with the FastQC tool and adapter sequence contamination removal with the CutAdapt tool. Because all base positions had first-quartile Phred scores greater than 20, trimming with FastQ Trimmer was not needed.
Reads were subsequently mapped to the Rattus norvegicus RN4 reference genome with TopHat (version 1.5.0) using an empirically determined insertion size of 210 base pairs.
The mapped reads were assembled into transcripts with Cufflinks (version 0.0.6) using quartile normalization.
Transcriptional datasets for each time point were pooled using CuffMerge.
Differences between strains at each time point were identified with CuffDiff.
Genome_build: RN4
Supplementary_files_format_and_content: Files containing CuffDiff results of gene differential expression testing (between strains, at each time point). In order, the columns indicate (A) tested object identifier (ID; here, equivalent to gene ID), (B) gene ID, (C) Rat Genome Database (RGD) gene ID, (D) genomic locus, (E) sample 1 (Sprague-Dawley, SD), (F) sample 2 (athymic nude, AN), (G) test status (OK = test successful), (H) FPKM for sample 1 (SD), (G) FPKM for sample 2 (AN), (H) log2(fold change) = log2(FPKM(SD)/FPKM(AN)), (I) test statistic, (J) p value, (K) q value, (L) statistically significant (if q<0.05).
 
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
 
Platform ID GPL14844
Series (1)
GSE62760 T Cell Deficiency in Spinal Cord Injury: Altered Locomotor Recovery and Whole-Genome Transcriptional Analysis
Relations
BioSample SAMN03145070
SRA SRX744902

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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