|
| Status |
Public on May 01, 2010 |
| Title |
Spi-2, bio rep 5 |
| Sample type |
RNA |
| |
|
| Source name |
100-200 motor neurons, sacral spinal cord, 2 days post injury
|
| Organism |
Rattus norvegicus |
| Characteristics |
injury stage: Spinal 2 days
gender: male
strain: Wistar
cell type: motor neuron
|
| Treatment protocol |
Injury: Laminectomy of lumbar vertebra L2-L3, spinal cord transect at S2 and 1-2mm of spinal cord tissue removed. Wound closed suturing muscles, muscle fascia and skin separately. Pain relieved with buprenorfin the first 48 hours. Spi-0 (Control): Sacral spinal cord removed and immediately frozen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cords were snap frozen in liquid nitrogen, cryosectioned into 10 micro meter slices, which were mounted onto POL-membrane metal frame slides (Leica) and fluorescently identied motor neurons were laser microdissected into a collector tube. Total RNA was extrated using the Picopure RNA isolation kit (Arcturus), which were then subject to a two round amplification using the RiboAmp HS RNA amplification kit (Arcturus) according to manufactors instructions. A DNAse treatment was included in the isolation protocol.
|
| Label |
biotin
|
| Label protocol |
Motor neurons retrogradely labelled with flourogold injected into the muscle and intra peritoneally 5-7 days prior to cell extraction.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45 °C on Affymetrix Rat Genome 230 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from motor neurons of the sacral rat spinal cord 2 days post transection
|
| Data processing |
Expression values were calculated using R and Bioconductor. RMA expression summaries were calculated based on PM intensity values that were normalised (linear quantile plus quantile projection) and background subtracted (global minimization) (Ryge et al, Plos One, 2008). The genes were filtered prior to analysis such that only probe sets annotated in the Ensembl database was included (using biomaRt bioconductor package), so the probe set was reduced from 31099 to 12919.
|
| |
|
| Submission date |
Dec 29, 2009 |
| Last update date |
Jan 04, 2010 |
| Contact name |
Jesper Ryge |
| E-mail(s) |
jesper.ryge@epfl.ch
|
| Phone |
+46707146879
|
| Organization name |
karolinska institutet
|
| Department |
neuroscience
|
| Lab |
mammalian locomotor lab
|
| Street address |
retziusvag 8
|
| City |
stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE19701 |
Time series gene expression data from adult rat tail MNs following spinal cord transection |
|
