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| Status |
Public on Dec 16, 2014 |
| Title |
Next Generation Sequencing (NGS) of zebrafish larvae transcriptome by 2,2',4,4'-tetrabromodiphenyl ether (BDE47) treatment |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: We report the application of NGS for profiling the impacts of BDE47 exposure on the transcriptome of zebrafish larvae.
Methods: mRNA 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, 2235 transcripts were affected after 500 μg/l exposure, in which 1338 were up-regulated and 897 were down-regulated, and 552 transcripts were affected after 5 μg/l exposure, in which 155 were up-regulated and 397 were down-regulated. High concentration of BDE47 exposure resulted in more up-regulated genes.
Conclusions: This study provides a framework for the application of high-throughput RNA sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval transcriptome.
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| Overall design |
Examination of zebrafish larvae transcriptomes with vehicle and 2 different concentrations of BDE47 treatments.
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| Contributor(s) |
Xu T, Zhao J |
| Citation(s) |
25614096 |
| Submission date |
Jul 31, 2014 |
| 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 (3) |
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| Relations |
| BioProject |
PRJNA257195 |
| SRA |
SRP045168 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE59968_Counts_Normalized.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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