Comment[ArrayExpressAccession]	E-GEOD-52500
MAGE-TAB Version	1.1						
Public Release Date	2013-11-20
Investigation Title	Gene expression data from rat cochlear lateral wall after 3NP damage						
Comment[Submitted Name]	Gene expression data from rat cochlear lateral wall after 3NP damage
Experiment Description	A rat model of acute mitochondrial dysfunction in the cochlea is created by applying an irreversible mitochondrial complex II enzyme inhibitor, 3-NP, directly to the round window membrane. Treatment with 300 mM 3-NP results in temporary hearing loss (temporary threshold shift (TTS) model), whereas treatment with 500 mM 3-NP results in profound and permanent hearing loss (permanent threshold shift (PTS) model. Either treatment results with a primary histological change in the lateral wall spiral ligament. Because local ATP deprivation in the inner ear results from inhibition of inner ear mitochondrial function, this model replicates the etiology of inner ear energy failure caused by ATP deprivation due to inner ear ischemia. We used microarrays to detail the global programme of gene expression in the damaged cochlear lateral wall by 3NP and identified distinct classes of up-regulated/ down-regulated genes during the process. One and three day after administrated either 300 mM of 3-NP (TTS-1d and TTS-3d, respectably) or saline (Ctrl-1d and Ctrl-3d, respectably), rat cochear lateral wall in the apical side of the basal turn was harvested for RNA extraction and hybridization on Affymetrix microarrays.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Fujioka	Tatsuo					
Person First Name	Masato	Matsunaga					
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	Keio University School of Med						
Person Address	Otorhinolaryngology, Keio University School of Med, 35 Shinanomachi Shinjuku, Tokyo, Japan						
Person Roles	submitter						
Protocol Name	P-GSE52500-1	P-GSE52500-5	P-GSE52500-6	P-GSE52500-2	P-GSE52500-3	P-GSE52500-4	P-GSE52500-7
Protocol Description	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. ID_REF =  VALUE = Signal ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = 	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Expression Array using Affymetrix genechip hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	After general anesthesia with pentobarbital (30–40 mg/kg, i.p.) and the local administration of lidocaine (1%), an incision was made posterior to the left pinna near the external meatus. The left otic bulla was opened and the round window niche was infused with 3-NP (500 mM or 300 mM) dissolved in saline (pH adjusted to 7.4 with NaOH). Infusion with saline alone was used as a control. Following treatment, and before the wound was closed, a small piece of gelatin was placed onto the niche to keep the solution in place and to allow for head movement after the animals awoke. The right cochlea was surgically destroyed to avoid cross-hearing during the recording of auditory brain-stem responses. The second turn of the lateral wall (excluding the stria vascularis) was harvested under the dissection microscope.	Female Sprague-Dawley rats weighing between 180 g and 210 g (8–10 weeks old) were purchased and bread in a SPF graded clean room.	Trizol extraction of total RNA was performed according to the manufacturer's instructions.	GeneChips were scanned using Molecular Dynamicfs GenePix4000A Lucida Module1(Amersham parmacia biotech Ludica base).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TREATMENT	TIME					
Experimental Factor Type	treatment	time					
Comment[SecondaryAccession]	GSE52500						
Comment[GEOReleaseDate]	2013-11-20						
Comment[ArrayExpressSubmissionDate]	2013-11-19						
Comment[GEOLastUpdateDate]	2013-11-21						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-52500.sdrf.txt