|
| Status |
Public on Feb 16, 2021 |
| Title |
Control1_region4 |
| Sample type |
SRA |
| |
|
| Source name |
spinal cord at lesion (~cervical level 4), including gray and white matter
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Long-Evans
tissue: spinal cord
age: ~6-8 months
genotype: WT
treatment: spinal cord injury, electrode implant
|
| Treatment protocol |
All animals (control and treatment) were given a hemicontusion injury at cervical level 4 using an Ohio State Impact Device calibrated to cause a displacement of 0.7mm. This incomplete injury causes a deficit in the use of the animal’s forelimb. Two weeks after injury all animals were implanted with an electrode array into motor cortex on the contralateral side to the injury. Approximate coordinates of the craniotomy were 5mm anterior to 1mm posterior of bregma, and 1-4mm lateral to the midline. One week after implantation, the efficacy of the electrodes to activate CST neurons was determined by measuring the threshold current for evoking forelimb movements on the lesioned side. Experimental animals were stimulated though the cortical channel that elicited the clearest forelimb movement at the lowest current threshold. Stimulation lasted for one week; control animals received sham stimulation (e.g. hooked up to stimulator with no current). Animals were stimulated for 5 hours a day at a frequency of 10 Hz for cycles of 5 minutes on/2 minutes off at 80% of movement threshold.
|
| Growth protocol |
Four adult female Long-Evans rats weighing 275-350 grams were kept on 12 hour light/dark cycle with ad limbitum access to food and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were euthanized and sections (outlined above) were quickly dissected out and snap frozen in liquid nitrogen. Tissue was homogenized and complete RNA was isolated using an RNAeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
Weill Cornell Epigenomics Core constructed the library per their standard Illumina methods for TruSeq Stranded Total-RNA protocol (citation: STAR: ultrafast universal RNA-seq aligner. Dobin, A. et al. Bioinformatics. 2012. 29 (1): 15-21.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The quality of all sequenced samples was analyzed using FastQC.The assessment results were summarized and visualized using MultiQC 1.6.
Reads were mapped to the Rnor6. Mapping and transcript assembly were performed with TopHat v2.1.0 and Cufflinks v2.2.1 respectively using default parameters.
We removed genes with FPKM <1 across all samples, as these genes were not expressed or were expressed at very low levels in all samples. To avoid inflation ratio, gene FPKM values < 0.1 were set to 0.1.
Genome_build: Rnor6
Supplementary_files_format_and_content: Matrix table with FPKM value for every gene and every sample
|
| |
|
| Submission date |
Aug 03, 2020 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Haichao Wei |
| E-mail(s) |
[email protected]
|
| Phone |
3462479690
|
| Organization name |
UTHealth
|
| Street address |
1825 Pressler St., SRB 637.C
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE155610 |
Transcriptome of Subcortical White Matter and Spinal Cord After Spinal Injury and Cortical Stimulation |
|
| Relations |
| BioSample |
SAMN15706092 |
| SRA |
SRX8873519 |
