|
| Status |
Public on Dec 31, 2015 |
| Title |
stimulated WAR rat, biological rep4 |
| Sample type |
RNA |
| |
|
| Source name |
WAR rats exposed to auditory stimulation
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar audiogenic rat (WAR)
strain provider: School of Medicine of Ribeirão Preto (Brazil)
gender: male
age: 12 weeks
body weight: ~230 g
exposed to: auditory stimulation
tissue: inferior colliculus (IC)
|
| Treatment protocol |
The animals were free of ear infection. To rapidly confirm normal hearing, we used the bilateral finger friction test in all cases. The animals in both models were exposed to auditory stimulation, and 60 min after the seizures, we harvested the IC for all gene expression analyses. As controls, normal Wistar rats and Syrian hamsters were exposed to the same stimulation according to the identical procedure.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using TRIZOL (Gibco BRL, Gaithersburg, MD, USA) following further RNA purification using an RNeasy Mini Kit for RNA clean-up (Qiagen Sicences, Maryland, USA). RNA quantification and quality was then assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), to test the integrity of the 18S and 28S rRNA bands, and samples with an RNA integrity number (RIN) > 8.0 were used.
|
| Label |
biotin
|
| Label protocol |
Microarray analysis was performed in the Cancer Research Center (CIC) of Salamanca according to standard procedures. Label protocol was performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA).
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| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized to GeneChip® Zebrafish Genome Array (Affymetrix). Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
|
| Description |
stim WAR 14.7_rep4
|
| Data processing |
The RMA (Robust Multi-array Analysis) algorithm was used for background correction and normalization of fluorescent hybridization signals of the microarrays, both at internal (intra-microarrays) and comparative (inter-microarrays) levels. We used Bioconductor and R as computational tools (www.bioconductor.org), to apply RMA to the data set of 12 microarray hybridizations including six different biological replicas corresponding to each of the different experimental groups under study (Control and Morphine). After quantitation of expression level of each probe set in all microarrays analyzed, the SAM algorithm was used to identify probe sets displaying significant differential expression when comparing the treat samples to it controls, using a False Discovery Rate (FDR) of 10% or less as significant.
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| |
|
| Submission date |
Oct 19, 2015 |
| Last update date |
Dec 31, 2015 |
| Contact name |
Raquel E. Rodriguez |
| E-mail(s) |
requelmi@usal.es
|
| Phone |
+34-923294500
|
| Organization name |
Institute of Neurosciences of Castilla y León
|
| Department |
-
|
| Lab |
13
|
| Street address |
C/ Pintor Fernando Gallego, 1
|
| City |
Salamanca |
| State/province |
Salamanca |
| ZIP/Postal code |
37007 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE74150 |
Changes in the gene expression in the inferior colliculus of the sound stimulated rats both Wistar and the strain susceptible to audiogenic seizures WAR |
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