|
| Status |
Public on Jun 27, 2015 |
| Title |
C57BL/6 sipnal cord, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
C57BL/6 lesioned spinal cord, 24 hours after injury
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
genotype/variation: wild type
age: 8-12 weeks
tissue: Spinal cord
|
| Treatment protocol |
Spinal cord contusion of 50 kdyn was performed using the Infinite Horizon SCI device (Precision Systems & Instrumentation).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cord segments of 6 mm-long centered over the lesion were rapidly dissected, frozen in liquid nitrogen, and stored at -80°C until RNA extraction. Total RNA was isolated by TRI Reagent and purified with the GenElute mammalian total RNA miniprep kit (Sigma-Aldrich Canada Ltd.).
|
| Label |
biotin
|
| Label protocol |
Two hundred nanograms of total RNA was labeled using the Ambion® WT Expression Kit protocol, as described by the manufacturer (Affymetrix, Santa Clara, CA). The quality of total RNA, cDNA synthesis, cRNA amplification, and cDNA fragmentation was monitored by microcapillary electrophoresis (Bioanalyzer 2100, Agilent Technologies).
|
| |
|
| Hybridization protocol |
Five µg of fragmented single-stranded cDNA was hybridized for 16 hours at 45°C with constant rotation on a GeneChip® Mouse Gene 1.0 ST Array (Affymetrix). After hybridization, were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol FS450_0007).
|
| Scan protocol |
Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix)
|
| Data processing |
Images were extracted with the GeneChip Operating Software (Affymetrix GCOS v1.4). Quality control of microarrays was performed using the AffyQCReport software. Background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA). Data analysis was performed using the AffylmGUI Graphical User Interface for the LIMMA microarray package (Wettenhall et al., 2006), and Partek Genomics Suite (Partek Incorporated)
|
| |
|
| Submission date |
Jun 26, 2015 |
| Last update date |
Jun 27, 2015 |
| Contact name |
Steve Lacroix |
| E-mail(s) |
[email protected]
|
| Organization name |
Centre de recherche du Centre hospitalier universitaire (CHU) de Québec - CHUL
|
| Department |
Médecine moléculaire
|
| Street address |
2705, boul. Laurier
|
| City |
Québec |
| State/province |
Québec |
| ZIP/Postal code |
G1V 4G2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE70302 |
Gene expression data of C57BL/6, Il1a-knockout and Il1b-knockout mice at 24 hours after spinal cord injury |
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