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| Status |
Public on Aug 21, 2019 |
| Title |
Tissue-specific transcriptomes reveal gene expression trajectories in two maturing skin epithelial layers in zebrafish embryos |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We purified (FACS) and profiled (RNA-Seq) zebrafish embryo skin cells vs. nonskin cells at three early developmental stages. At two of the stages, we further purified and profiled two distinct epithelial layers of the skin: the periderm and basal cells. Our comprehensive expression analysis provides the first reported transcriptomes of these two cell types, reveals gene expression dynamics in space and time, and identifies common and distinct features of epithelial maturation in the two layers. Given the conserved nature of skin development, we believe our study to be of interest to those studying skin in other vertebrates.
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| Overall design |
At each of 20 SS, 52 hpf, and 72 hpf, we used krt4:dsRed transgenic zebrafish embryos and FACS to prepare and run two RNA-Seq conditions: all skin vs. nonskin1, with two replicates for each condition. At each of 52 hpf and 72 hpf, we used krt4:dsRed;krt5:GFP transenic zebrafish embryos and FACS to prepare and run three RNA-Seq conditions: periderm vs. basal cells vs. nonskin2, with two replicates for each condition, except 52 hpf nonskin2 has only one replicate.
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| Web link |
https://zfishskin.net/
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| Contributor(s) |
Cokus SJ, Wang F, Sagasti A |
| Citation(s) |
31431477 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R21 EY024400 |
The morphogenesis of actin-based structures in mucosal epithelia |
UNIVERSITY OF CALIFORNIA LOS ANGELES |
Alvaro Sagasti |
| R01 GM122901 |
Cytoskeletal control of microridge morphogenesis on mucosal epithelial cells of the zebrafish skin |
UNIVERSITY OF CALIFORNIA LOS ANGELES |
Alvaro Sagasti |
| R01 AR064582 |
Peripheral Territory Establishment By Zebrafish Somatosensory Neurons |
UNIVERSITY OF CALIFORNIA LOS ANGELES |
Alvaro Sagasti |
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| Submission date |
Jun 06, 2019 |
| Last update date |
Aug 24, 2019 |
| Contact name |
Shawn J. Cokus |
| Organization name |
UCLA
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| Street address |
UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (2) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
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| Samples (23)
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| GSM3855893 |
20 SS, all skin, replicate B |
| GSM3855894 |
52 hpf, nonskin1, replicate A |
| GSM3855895 |
52 hpf, nonskin1, replicate B |
| GSM3855896 |
52 hpf, all skin, replicate A |
| GSM3855897 |
52 hpf, all skin, replicate B |
| GSM3855898 |
52 hpf, nonskin2, only replicate |
| GSM3855899 |
52 hpf, basal cells, replicate A |
| GSM3855900 |
52 hpf, basal cells, replicate B |
| GSM3855901 |
52 hpf, periderm, replicate A |
| GSM3855902 |
52 hpf, periderm, replicate B |
| GSM3855903 |
72 hpf, nonskin1, replicate A |
| GSM3855904 |
72 hpf, nonskin1, replicate B |
| GSM3855905 |
72 hpf, all skin, replicate A |
| GSM3855906 |
72 hpf, all skin, replicate B |
| GSM3855907 |
72 hpf, nonskin2, replicate A |
| GSM3855908 |
72 hpf, nonskin2, replicate B |
| GSM3855909 |
72 hpf, basal cells, replicate A |
| GSM3855910 |
72 hpf, basal cells, replicate B |
| GSM3855911 |
72 hpf, periderm, replicate A |
| GSM3855912 |
72 hpf, periderm, replicate B |
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| Relations |
| BioProject |
PRJNA547573 |
| SRA |
SRP200656 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE132304_RAW.tar |
6.9 Gb |
(http)(custom) |
TAR (of TAR) |
| GSE132304_ZFishSkin-MASTER-WORKBOOK-20190605.xlsx |
251.9 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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