Comment[ArrayExpressAccession]	E-GEOD-40745
MAGE-TAB Version	1.1			
Public Release Date	2013-04-02
Investigation Title	Transcriptomic analyses of Myc-induced zebrafish liver cancer			
Comment[Submitted Name]	Transcriptomic analyses of Myc-induced zebrafish liver cancer
Experiment Description	To study the characteristics and mechanisms of Myc-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 ribosome proteins were overwhelmingly up-regulated in the Myc-induced liver tumors. Cross-species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc-induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma (HCC). Thus, our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Transcriptome profiling of tumor samples (M+D+) and control samples (M-D-, M+D-, M-D+) were generated by deep sequencing, each in duplicates, using 3' RNA-SAGE on the SOLiD system.			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	Zheng	Li	Zheng	Gong
Person First Name	Weiling	Zhen	Weiling	Zhiyuan
Person Email	dbszwl@nus.edu.sg			
Person Affiliation	National University of Singapore			
Person Address	National University of Singapore, 21 Lower Kent Ridge Road, Singapore, Singapore			
Person Roles	submitter			
Protocol Name	P-GSE40745-3	P-GSE40745-1	P-GSE40745-2	
Protocol Description	The SOLiD-generated RNA-Seq reads were 27 bp in length. An initial filtering process was performed to remove any non-desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database (Release 39) allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million (TPM) to faciliate comparison among different samples. Genome_build: RefSeq Release 39 Supplementary_files_format_and_content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.	Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6-L tanks with around 25 adults and water was changed every other day.	Total RNA was extracted using TRIzol (Invitrogen). Library construction was conducted by Mission Biotech (Taiwan) following the standard ABI SOLiD protocol.	
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	
Experimental Factor Name	TREATMENT	GENOTYPE		
Experimental Factor Type	treatment	genotype		
Publication Title	A transgenic zebrafish liver tumor model with inducible Myc expression reveals conserved Myc signatures with mammalian liver tumors.			
Publication Author List	Li Z, Zheng W, Wang Z, Zeng Z, Zhan H, Li C, Zhou L, Yan C, Spitsbergen JM, Gong Z			
PubMed ID	23038063			
Publication DOI	10.1242/dmm.010462			
Comment[SecondaryAccession]	GSE40745			
Comment[GEOReleaseDate]	2013-04-02			
Comment[ArrayExpressSubmissionDate]	2012-09-10			
Comment[GEOLastUpdateDate]	2013-04-18			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[SecondaryAccession]	SRP015680			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR566689-SRR566696			
SDRF File	E-GEOD-40745.sdrf.txt