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| Status |
Public on Dec 17, 2013 |
| Title |
Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor, next generation sequencing-based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless, they all significantly correlate with advanced or very advanced human hepatocellular carcinoma (HCC). Molecular signature from each oncogene-induced zebrafish liver tumor correlated with only a small subset of human HCC samples, and they share conserved up-regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs, suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus, these transgenic zebrafish models with well-defined oncogene-induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup.
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| Overall design |
Transcriptome profiling of Myc tumor sample (X-M+D+) and control samples (X-M-D-, X-M+D-, X-M-D+), xmrk tumor sample (X+M-D+) and control samples (X-M-D-, X+M-D-, X-M-D+), were generated by deep sequencing, using 3' RNA-SAGE on SOLiD system
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| Contributor(s) |
Zheng W, Li Z, Gong Z |
| Citation(s) |
24633177 |
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| Submission date |
Dec 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Weiling Zheng |
| E-mail(s) |
zhengweiling.echo@gmail.com
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| Organization name |
National University of Singapore
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| Street address |
Science Drive 4
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| City |
Singapore |
| ZIP/Postal code |
117543 |
| Country |
Singapore |
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| Platforms (1) |
| GPL10658 |
AB SOLiD System 3.0 (Danio rerio) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA231764 |
| SRA |
SRP034513 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53342_RAW.tar |
540.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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