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| Status |
Public on Jan 12, 2017 |
| Title |
Next Generation Sequencing (NGS) of zebrafish larvae microRNA expression profilling by 2,2',4,4'-tetrabromodiphenyl ether (BDE47) treatment |
| Organism |
Danio rerio |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae.
Methods: miRNA profiles of 6-day-old BDE47-treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: Compared BDE47 treatments with solvent control, a dozen of validated zebrafish miRNAs, including dre-miR-142a-3p, dre-miR-142b-5p, dre-miR-144-3p, dre-miR-146a, dre-miR-190a, dre-miR-219-5p, dre-miR-301b-3p, dre-miR-459-5p, rno-miR-33-5p, dre-miR-735-3p, and dre-miR-735-5p, significantly changed their expressions.
Conclusions: This study provides a framework for the application of high-throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling.
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| Overall design |
Examination of zebrafish larvae miRNA expression profilings with blank, vehicle and 2 different concentrations of BDE47 treatments.
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| Contributor(s) |
Xu T, Zhao J |
| Citation(s) |
28072866 |
| Submission date |
Jul 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ting Xu |
| E-mail(s) |
412_xuting@tongji.edu.cn
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| Organization name |
Tongji University
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| Street address |
No. 1239 Road Siping
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA335352 |
| SRA |
SRP079896 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84845_small_RNA_Normalized.txt.gz |
6.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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