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| Status |
Public on Aug 12, 2014 |
| Title |
Transcriptomes of the Cochlear Inner and Outer Hair Cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
The transcriptome is the complete set of all RNA transcripts produced by the genome in a cell and reflects the genes that are being actively expressed. Transcriptome analysis is essential for understanding the genetic mechanism controlling the phenotype of a cell.
Using DNA microarray technique we examined transcriptomes of 2,000 individually collected inner (IHCs) and outer hair cells (OHCs), two types of auditory sensory cells critical for hearing. Among approximately 16,645 and 17,711 transcripts considered to be expressed, 1,296 and 256 genes showed significant differential expression in IHCs and OHCs, respectively. The top ten differentially expressed genes include Slc17a8, Dnajc5b, Slc1a3, Atp2a3, Osbpl6, Slc7a14, Bcl2, Bin1, Prkd1, Map4k4 in IHCs, and Slc26a5, C1ql1, Strc, Dnm3, Plbd1, Lbh, Olfm1, Plce1, Tectb, Ankrd22 in OHCs. Many unknown sequences and non-coding RNAs were also expressed in hair cells. The differentially expressed genes underlie the genetic mechanism for unique functions of IHCs and OHCs.
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| Overall design |
The total RNA was extracted from the collected pools of single outer hair cells (OHCs) and inner hair cells (IHCs). Their whole-genome transcriptome expression was detected using GeneChip microarray analysis. The analysis and comparison between OHC and IHC allow us to determine what genes are expressed and what genes are uniquely or differential expressed in each population.
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| Contributor(s) |
Liu HZ, Pecka JL, Zhang Q, Soukup G, Beisel KW, He DZ |
| Citation(s) |
25122905, 26974322 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 DC004696 |
Biophysics and Development of Cochlear Hair Cells: BIOPHYSICS AND DEVELOPMENT OF COCHLEAR OUTER HAIR CELLS: Biophysics and Development of Cochlear Hair Cells: BIOPHYSICS AND DEVELOPMENT OF COCHLEAR OUTER HAIR CELLS: BIOPHYSICS AND DEVELOPMENT OF COCHLEAR OUTER HAIR CELLS: Biophysics and Development of Cochlear Hair Cells: Biophysics and Development of Cochlear Hair Cells: Biophysics and Development of Cochlear Hair Cells: Biophysics and Development of Cochlear Hair Cells: Biophysics and Development of Cochlear Hair Cells: Biophysics and Development of Cochlear Hair Cells: Biophysics and Development of Cochlear Hair Cells |
CREIGHTON UNIVERSITY |
David Z.Z. He |
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| Submission date |
Apr 17, 2014 |
| Last update date |
Feb 21, 2018 |
| Contact name |
David Z.Z. He |
| E-mail(s) |
hed@creighton.edu
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| Phone |
14022801409
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| Organization name |
Creighton University
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| Department |
Department of Biomedical Sciences
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| Street address |
2500 California Plaza
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| City |
Omaha |
| State/province |
Nebraska |
| ZIP/Postal code |
68178 |
| Country |
USA |
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| Platforms (1) |
| GPL16570 |
[MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array [transcript (gene) version] |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA244830 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56866_HC-Transcriptomes.xlsx.gz |
4.4 Mb |
(ftp)(http) |
XLSX |
| GSE56866_RAW.tar |
56.6 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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