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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 14, 2026 |
| Title |
https://www.ncbi.nlm.nih.gov/geo/ |
| Organism |
Danio rerio |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Neural crest cells are a transient, multipotent population that gives rise to diverse structures during vertebrate embryonic development, including craniofacial cartilage and pigment cells. Although the transcriptional regulation of neural crest development is well characterized, the role of microRNAs remains less understood. Using a double-transgenic zebrafish model expressing fluorescent reporters under the sox10 promoter, combined with fluorescence-activated cell sorting and RNA sequencing, we identified microRNAs enriched in neural crest cells. We focused on miR-133a-3p and miR-338-3p, previously linked to tumor suppression, to explore their developmental roles. The overexpression of either microRNA led to craniofacial cartilage malformations and reduced melanophore number, accompanied by decreased expression of key regulators including sox9b, sox10, and runx3. Reporter assays confirmed direct targeting of the sox9b 3′untranslated region. In addition, miR-338-3p overexpression increased neural crest cell numbers, suggesting a role in proliferation. These findings uncover novel functions for miR-133a-3p and miR-338-3p in vertebrate craniofacial and pigment cell development, highlighting shared regulatory features between embryogenesis and tumorigenesis.
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| Overall design |
Small RNA-seq profiling of neural crest, non-neural crest, and whole-embryo samples from Tg(sox10:eGFP,mRFP) zebrafish at 16 and 28 hpf.
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| Contributor(s) |
Steeman TJ, Torres M, Weiner AM, Rubiolo JA, Sánchez LE, Coux G, Calcaterra NB |
| Citation(s) |
41997877 |
| BioProject |
PRJNA1278791 |
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| Submission date |
Jun 20, 2025 |
| Last update date |
May 06, 2026 |
| Contact name |
Tomás José Steeman |
| E-mail(s) |
steeman.tj@gmail.com
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| Organization name |
IBR
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| Street address |
Ocampo y Esmeralda
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| City |
Rosario |
| State/province |
Santa Fe |
| ZIP/Postal code |
2000 |
| Country |
Argentina |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (4)
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| GSM9059131 |
Small RNA-Seq of Danio rerio: FACS-sorted neural crest cells at 16 hpf |
| GSM9059132 |
Small RNA-Seq of Danio rerio: FACS-sorted non-neural crest cells at 16 hpf |
| GSM9059133 |
Small RNA-Seq of Danio rerio: FACS-sorted neural crest cells at 28 hpf |
| GSM9059134 |
Small RNA-Seq of Danio rerio: FACS-sorted non-neural crest cells at 28hpf |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE300363_normCountsA23.csv.gz |
4.9 Kb |
(ftp)(http) |
CSV |
| GSE300363_normCountsA56.csv.gz |
2.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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