|
| Status |
Public on Apr 26, 2023 |
| Title |
P32, hearing, apex, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
P32 hearing spiral ganglion, apical half
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: P32
condition: hearing
tissue: spiral ganglion
cochlear location: apex
|
| Treatment protocol |
Male and female Sprague-Dawley rats were injected with kanamycin (400 mg/kg, i.p.) once daily from P8-P16. Cochleae were collected from injected and littermate control (uninjected) rats at P32 or P60. Temporal bones were rapidly removed and placed in ice-cold phosphate-buffered saline, pH 7.4 (PBS) for dissection. The bony capsule and spiral ligament were dissected away from the cochlea. The remaining tissue was divided into apical and basal portions and the organ of Corti was separated from the spiral ganglion. Four to six ganglia were used for each biological replicate.
|
| Growth protocol |
Sprague-Dawley rats from our breeding colony or from pregnant dams purchased from Envigo were used. Rats of both sexes were used. The day of birth was designated as P0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The Rneasy mini-kit (Qiagen) was used to extract total RNA from the isolated spiral ganglia. RNA was amplified (3-4X) using an Ambion Message Amp II kit. cDNA was then synthesized using a SuperScript II Reverse Transcriptase Second Strand kit.
|
| Label |
Cy3
|
| Label protocol |
cDNA was labeled using Cy3-coupled random nonamers (Roche NimbleGen).
|
| |
|
| Hybridization protocol |
Labeled cDNA was hybridized for 20 hours to Roche NimbleGen HD2 rat gene expression arrays. Each biological replicate was analyzed in triplicate (3 technical replicates).
|
| Scan protocol |
Arrays were scanned on an Axon GenePix 4200A microarray scanner (Molecular Devices).
|
| Description |
P32HA2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate
|
| Data processing |
Pair files were generated and Lasergene ArrayStar (version 17, DNASTAR) was used for noise subtraction and RMA quantile normalization. Normalized signal intensities were used to calculate fold changes between conditions.
RMA-normalized-data_all-genes.txt is represented in the Data table (represents the normalized signal intensities for all genes present on the microarray).
RMA-normalized-data_expr-only.txt is linked as a supplementary file on the Series record (represents the normalized signal intensities for only the genes we considered to be expressed).
|
| |
|
| Submission date |
Dec 03, 2021 |
| Last update date |
Apr 26, 2023 |
| Contact name |
Steven Haym Green |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Iowa
|
| Department |
Biology
|
| Lab |
Green
|
| Street address |
143 Biology Building
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52246 |
| Country |
USA |
| |
|
| Platform ID |
GPL19519 |
| Series (1) |
| GSE190146 |
Microarray expression profiling of the spiral ganglion of hearing and deafened rats |
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