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| Status |
Public on Mar 26, 2014 |
| Title |
Gene expression analysis of hair cell regeneration in the zebrafish lateral line |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However, non-mammalian animals (e.g. birds, amphibian and fish) regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates, we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA-Seq analyses on regenerating support cells purified by fluorescence activated cell sorting (FACS). The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration, because these cells can be acutely killed by exposure to neomycin, after which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. Tg(sqET20) larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 days post fertilization (dpf) Tg(sqET20) larvae at 1, 3 and 5 hours post neomycin treatment, as well as from a non-treated control.
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| Overall design |
Transgenic zebrafish Tg(sqET20) larvae at 5 days post fertilization were exposed to neomycin, dissociated, and FACS sorted into GFP positive and GFP negative populations at 1, 3, and 5 hours following treatment, along with a mock treated 1 hr control. The experiment was performed in triplicate, for a total of 24 samples.
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| Contributor(s) |
Jiang L, Romero-Carvajal A, Haug JS, Seidel CW, Piotrowski T |
| Citation(s) |
24706903 |
| Submission date |
Mar 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris W Seidel |
| E-mail(s) |
seidel@phageT4.org
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| Phone |
816 926 9054
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| Organization name |
Stowers Institute
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| Department |
Genomics
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| Lab |
Seidel
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| Street address |
1000 E 50th St
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| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA242641 |
| SRA |
SRP040561 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56176_fpkm.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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