|
| Status |
Public on Aug 12, 2014 |
| Title |
Outer hair cells-1 month-1 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse cochlea at the age of one month
|
| Organism |
Mus musculus |
| Characteristics |
strain: CBA/J
cell type: outer hair cells in the cochlea
age: 25-35 days old
|
| Treatment protocol |
The basilar membrane together with the organ of Corti was isolated and transferred to an enzymatic digestion medium in a small Petri dish. The enzymatic digestion medium contained 1 ml L-15 and 1 mg Collegene IV (Sigma). After 5 min incubation at room temperature, the tissue was transferred to a small plastic chamber (0.8 ml in volume) containing enzyme-free culture medium (Leibovitz's L-15, 7.35 pH, 300 mOsm). Hair cells were separated after gentle trituration of the tissue with a small pipette.
|
| Growth protocol |
CBA/J mice were used at the age of 25-35 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from approximately 2,000 IHCs and OHCs separately suspended in RNALater were extracted and purified using the Qiagen miRNeasy Mini Kit according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Amplification and synthesis of cDNA were completed using the NuGEN Ovation Pico WTA System V2.
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| |
|
| Hybridization protocol |
The transcriptome profile of the two cell populations was determined by GeneChip microarray analysis (Affymetrix, Santa Clare, CA, USA). Synthesis of cDNA, hybridization to chips, and washes were performed according to the manufacture’s protocol.
|
| Scan protocol |
GeneChips were scanned at 3 µm density with a GeneArray Scanner (Affymetrix).
|
| Description |
Whole genome transcriptome expression in the outer hair cells at the age of one month of CBA/J mice
OHC-1
|
| Data processing |
The data was normalized by Affy program “Expression Console”. Mean fluorescence signal intensity for each probe was quartile normalized. The average of three mean signals for each gene probe was normalized to that for an added control oligonucleotide. Each gene probe was assessed for expression based on a Wilcoxon Rank-Sum test of the gene probe set signals compared to the distribution of signals from the background.
Please note that 18,240 transcripts (out of total 41,345 mouse RefSeq transcripts included in the microarray) were examined after excluding control sequences and judiciously setting a cutoff for background. Of those, 16,647 and 17,711 transcripts were considered "expressed" in IHCs and OHCs, respectively, and 16,117 transcripts were expressed in both cell populations ('HC-Transcriptomes.xlsx' available on Series record).
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| |
|
| Submission date |
Apr 17, 2014 |
| Last update date |
Aug 12, 2014 |
| Contact name |
David Z.Z. He |
| E-mail(s) |
hed@creighton.edu
|
| Phone |
14022801409
|
| Organization name |
Creighton University
|
| Department |
Department of Biomedical Sciences
|
| Street address |
2500 California Plaza
|
| City |
Omaha |
| State/province |
Nebraska |
| ZIP/Postal code |
68178 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE56866 |
Transcriptomes of the Cochlear Inner and Outer Hair Cells |
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