rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
36336,SRR390721,SRX112005,SRS282726,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HBx+HCP transgenic line,GSM850201,,source name:zebrafish liver|phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver,mRNA from HBx+HCP transgenic line,HBx+HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver,GSM850201,GSM850201: mRNA from HBx+HCP transgenic line; Danio rerio; RNA Seq,GSM850201 1,GSM850201: mRNA from HBx+HCP transgenic line,1,,GEO Accession:GSM850201,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,500Application ReadForward1,SRP009863,,,HBx+HCP.qual HBx+HCP.csfasta,SOLiD_native SOLiD_native,3946087000.0,78921740.0,GSM850201 r1,0:50,0:926148003;1:1112848138;2:1139608445;3:763770020;.:3712394,50,,,,,,,,,SRX112005,SRS282726,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.71816,,0.05681,,0.91727,,0.25279,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36337,SRR390720,SRX112004,SRS282725,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HCP transgenic line,GSM850200,,source name:zebrafish liver|phenotype:n1|strain:HCP transgenic|tissue:liver,mRNA from HCP transgenic line,HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:HCP transgenic|tissue:liver,GSM850200,GSM850200: mRNA from HCP transgenic line; Danio rerio; RNA Seq,GSM850200 1,GSM850200: mRNA from HCP transgenic line,1,,GEO Accession:GSM850200,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,500Application ReadForward1,SRP009863,,,HCP.qual HCP.csfasta,SOLiD_native SOLiD_native,4104044600.0,82080892.0,GSM850200 r1,0:50,0:944238890;1:1172273582;2:1207771613;3:775967445;.:3793070,50,,,,,,,,,SRX112004,SRS282725,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.70132,,0.05286,,0.94422,,0.26785,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36338,SRR390719,SRX112003,SRS282724,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HBx transgenic line,GSM850199,,source name:zebrafish liver|phenotype:n1|strain:HBx transgenic|tissue:liver,mRNA from HBx transgenic line,HBx count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:HBx transgenic|tissue:liver,GSM850199,GSM850199: mRNA from HBx transgenic line; Danio rerio; RNA Seq,GSM850199 1,GSM850199: mRNA from HBx transgenic line,1,,GEO Accession:GSM850199,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,500Application ReadForward1,SRP009863,,,HBx.qual HBx.csfasta,SOLiD_native SOLiD_native,3783924950.0,75678499.0,GSM850199 r1,0:50,0:909506019;1:1055965468;2:1075994223;3:739008253;.:3450987,50,,,,,,,,,SRX112003,SRS282724,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.70675,,0.04174,,0.94146,,0.22954,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36339,SRR390718,SRX112002,SRS282723,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from AB strain,GSM850198,,source name:zebrafish liver|phenotype:n1|strain:AB|tissue:liver,mRNA from AB strain,WT count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:AB|tissue:liver,GSM850198,GSM850198: mRNA from AB strain; Danio rerio; RNA Seq,GSM850198 1,GSM850198: mRNA from AB strain,1,,GEO Accession:GSM850198,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,500Application ReadForward1,SRP009863,,,WT.csfasta WT.qual,SOLiD_native SOLiD_native,5129652800.0,102593056.0,GSM850198 r1,0:50,0:1167298346;1:1421158274;2:1551481320;3:984758434;.:4956426,50,,,,,,,,,SRX112002,SRS282723,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.73072,,0.04843,,0.95574,,0.21796,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36506,SRR566696,SRX185761,SRS361914,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,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. Overall design: 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 three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: liver tumor M+D+,GSM1000561: M+D+ 2,GSM1000561,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline,M+D+ 2,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.,liver tumor M+D+,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.,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline,GSM1000561,GSM1000561: M+D+ 2; Danio rerio; RNA Seq,GSM1000561 1,,1,,GEO Accession:GSM1000561,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M+D+_2_QV.qual M+D+_2.csfasta,SOLiD_native SOLiD_native,1493416960.0,42669056.0,GSM1000561 r1,0:35,0:377247910;1:348861020;2:522134600;3:237405266;.:7768164,35,,,,,,,,,SRX185761,SRS361914,SRA058618,GEO,National University of Singapore,1,0.06244,,0.00306,,0.99567,,0.34618,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36507,SRR566695,SRX185760,SRS361913,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,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. Overall design: 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 three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: liver tumor M+D+,GSM1000560: M+D+ 1,GSM1000560,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline,M+D+ 1,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.,liver tumor M+D+,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.,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline,GSM1000560,GSM1000560: M+D+ 1; Danio rerio; RNA Seq,GSM1000560 1,,1,,GEO Accession:GSM1000560,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,,,1291539515.0,36901129.0,GSM1000560 r1,0:35,0:266006021;1:328523841;2:440474617;3:254266912;.:2268124,35,,,,,,,,,SRX185760,SRS361913,SRA058618,GEO,National University of Singapore,1,0.10629,,0.0044,,0.99239,,0.31953,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36508,SRR566694,SRX185759,SRS361912,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,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. Overall design: 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 three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver M D+,GSM1000559: M D+ 2,GSM1000559,,genotype:wildtype|tissue:liver|treatment:doxycycline,M D+ 2,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.,control liver M D+,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.,,genotype:wildtype|tissue:liver|treatment:doxycycline,GSM1000559,GSM1000559: M D+ 2; Danio rerio; RNA Seq,GSM1000559 1,,1,,GEO Accession:GSM1000559,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M-D+_2_QV.qual,SOLiD_native,1438423910.0,41097826.0,GSM1000559 r1,0:35,0:353104627;1:349496969;2:433338629;3:275089557;.:27394128,35,,,,,,,,,SRX185759,SRS361912,SRA058618,GEO,National University of Singapore,1,0.04748,,0.00442,,0.99425,,0.53794,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36509,SRR566693,SRX185758,SRS361911,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,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. Overall design: 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 three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver M D+,GSM1000558: M D+ 1,GSM1000558,,genotype:wildtype|tissue:liver|treatment:doxycycline,M D+ 1,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.,control liver M D+,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.,,genotype:wildtype|tissue:liver|treatment:doxycycline,GSM1000558,GSM1000558: M D+ 1; Danio rerio; RNA Seq,GSM1000558 1,,1,,GEO Accession:GSM1000558,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M-D+_1.csfasta,SOLiD_native,1284638285.0,36703951.0,GSM1000558 r1,0:35,0:328871758;1:317693850;2:402981931;3:233637468;.:1453278,35,,,,,,,,,SRX185758,SRS361911,SRA058618,GEO,National University of Singapore,1,0.10539,,0.00562,,0.99141,,0.37635,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36510,SRR566692,SRX185757,SRS361910,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,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. Overall design: 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 three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver M+D ,GSM1000557: M+D 2,GSM1000557,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1,M+D 2,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.,control liver M+D ,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.,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1,GSM1000557,GSM1000557: M+D 2; Danio rerio; RNA Seq,GSM1000557 1,,1,,GEO Accession:GSM1000557,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M+D-_2_QV.qual,SOLiD_native,1404966080.0,40141888.0,GSM1000557 r1,0:35,0:371691603;1:354481639;2:405221861;3:271978812;.:1592165,35,,,,,,,,,SRX185757,SRS361910,SRA058618,GEO,National University of Singapore,1,0.07869,,0.00455,,0.99253,,0.51508,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36511,SRR566691,SRX185756,SRS361909,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,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. Overall design: 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 three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver M+D ,GSM1000556: M+D 1,GSM1000556,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1,M+D 1,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.,control liver M+D ,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.,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1,GSM1000556,GSM1000556: M+D 1; Danio rerio; RNA Seq,GSM1000556 1,,1,,GEO Accession:GSM1000556,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M+D-_1_QV.qual M+D-_1.csfasta,SOLiD_native SOLiD_native,1286706820.0,36763052.0,GSM1000556 r1,0:35,0:252864341;1:338709089;2:436928155;3:256235022;.:1970213,35,,,,,,,,,SRX185756,SRS361909,SRA058618,GEO,National University of Singapore,1,0.12399,,0.00617,,0.98752,,0.50351,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36512,SRR566690,SRX185755,SRS361908,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,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. Overall design: 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 three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver M D ,GSM1000555: M D 2,GSM1000555,,genotype:wildtype|tissue:liver|treatment:n1,M D 2,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.,control liver M D ,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.,,genotype:wildtype|tissue:liver|treatment:n1,GSM1000555,GSM1000555: M D 2; Danio rerio; RNA Seq,GSM1000555 1,,1,,GEO Accession:GSM1000555,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M-D-_2_QV.qual M-D-_2.csfasta,SOLiD_native SOLiD_native,1337952770.0,38227222.0,GSM1000555 r1,0:35,0:391863829;1:347720340;2:312814682;3:283542736;.:2011183,35,,,,,,,,,SRX185755,SRS361908,SRA058618,GEO,National University of Singapore,1,0.04605,,0.00365,,0.99494,,0.51825,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36513,SRR566689,SRX185754,SRS361907,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,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. Overall design: 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 three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver M D ,GSM1000554: M D 1,GSM1000554,,genotype:wildtype|tissue:liver|treatment:n1,M D 1,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.,control liver M D ,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.,,genotype:wildtype|tissue:liver|treatment:n1,GSM1000554,GSM1000554: M D 1; Danio rerio; RNA Seq,GSM1000554 1,,1,,GEO Accession:GSM1000554,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M-D-_1.csfasta,SOLiD_native,1395143680.0,39861248.0,GSM1000554 r1,0:35,0:439852883;1:355203725;2:298639546;3:299770820;.:1676706,35,,,,,,,,,SRX185754,SRS361907,SRA058618,GEO,National University of Singapore,1,0.02094,,0.00123,,0.99784,,0.58426,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
37108,SRR924082,SRX316721,SRS472258,SRP026400,PRJNA210007,Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver,GSE48427,Transcriptome Analysis,In the present study we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure including oxidation reduction translation iron ion transport cell redox and homeostasis as well as related pathways in metabolism and diseases. Furthermore as there are currently no biomarker genes available for predicting arsenic exposure we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.,,pubmed:24176670;pubmed:23922661,,H2O treated zebrafish liver,GSM1177837,,source name:liver control|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control,H2O treated zebrafish liver,The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI RefSeq accession and expression levels in TPM.,liver control,3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.,Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control,GSM1177837,GSM1177837: H2O treated zebrafish liver; Danio rerio; RNA Seq,GSM1177837,,1,Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,GEO Accession:GSM1177837,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP026400,,,solid0518_20101014_Gong_1_SetA_F3_0_1H2O.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_1H2O.qual,SOLiD_native SOLiD_native,477311205.0,13637463.0,GSM1177837 r1,0:35,0:176467601;1:101093405;2:105775125;3:93265462;.:709612,35,,,,,,,,,SRX316721,SRS472258,SRA091803,GEO,National University of Singapore,1,0.02019,,0.01385,,0.9973,,0.64062,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-06-28,Adult,Adult,Liver,Liver and Biliary System
37109,SRR924081,SRX316720,SRS454027,SRP026400,PRJNA210007,Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver,GSE48427,Transcriptome Analysis,In the present study we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure including oxidation reduction translation iron ion transport cell redox and homeostasis as well as related pathways in metabolism and diseases. Furthermore as there are currently no biomarker genes available for predicting arsenic exposure we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.,,pubmed:24176670;pubmed:23922661,,Arsenic treated zebrafish liver,GSM1177836,,source name:liver arsenic|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium,Arsenic treated zebrafish liver,The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI RefSeq accession and expression levels in TPM.,liver arsenic,3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.,Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium,GSM1177836,GSM1177836: Arsenic treated zebrafish liver; Danio rerio; RNA Seq,GSM1177836,,1,Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,GEO Accession:GSM1177836,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP026400,,,solid0518_20101014_Gong_1_SetA_F3_QV_2_2Arsenic.qual solid0518_20101014_Gong_1_SetA_F3_2_2Arsenic.csfasta,SOLiD_native SOLiD_native,477279215.0,13636549.0,GSM1177836 r1,0:35,0:135280436;1:121477647;2:102046207;3:117826846;.:648079,35,,,,,,,,,SRX316720,SRS454027,SRA091803,GEO,National University of Singapore,1,0.0161,,0.00302,,0.99334,,0.51629,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-06-28,Adult,Adult,Liver,Liver and Biliary System
37130,SRR952910,SRX335554,SRS470625,SRP028848,PRJNA215326,Transcriptomic analyses of TCDD treated zebrafish liver,GSE49915,Transcriptome Analysis,To fully understand molecular toxicity of TCDD in an in vivo animal model adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes 10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle endocrine disruptors signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system,,pubmed:24204792,,DMSO,GSM1209643,,source name:liver|tissue:liver|genotype:wildtype sibling|treatment:DMSO,DMSO,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM.,liver,3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day.,Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:wildtype sibling|treatment:DMSO,GSM1209643,GSM1209643: DMSO; Danio rerio; RNA Seq,GSM1209643,,1,Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1209643,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP028848,,,solid0518_20101014_Gong_1_SetA_F3_0_2DMSO.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_2DMSO.qual,SOLiD_native SOLiD_native,409327205.0,11695063.0,GSM1209643 r1,0:35,0:136723730;1:95263220;2:87949986;3:88818989;.:571280,35,,,,,,,,,SRX335554,SRS470625,SRA098000,GEO,National University of Singapore,1,0.01735,,0.00647,,0.9946,,0.51324,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-08-15,Adult,Adult,Liver,Liver and Biliary System
37131,SRR952909,SRX335553,SRS470624,SRP028848,PRJNA215326,Transcriptomic analyses of TCDD treated zebrafish liver,GSE49915,Transcriptome Analysis,To fully understand molecular toxicity of TCDD in an in vivo animal model adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes 10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle endocrine disruptors signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system,,pubmed:24204792,,TCDD,GSM1209642,,source name:liver|tissue:liver|genotype:wildtype sibling|treatment:TCDD,TCDD,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM.,liver,3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day.,Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:wildtype sibling|treatment:TCDD,GSM1209642,GSM1209642: TCDD; Danio rerio; RNA Seq,GSM1209642,,1,Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1209642,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP028848,,,solid0518_20101014_Gong_1_SetA_F3_QV_1_2TCDD.qual solid0518_20101014_Gong_1_SetA_F3_1_2TCDD.csfasta,SOLiD_native SOLiD_native,627514895.0,17928997.0,GSM1209642 r1,0:35,0:214639659;1:142538233;2:131819822;3:137625000;.:892181,35,,,,,,,,,SRX335553,SRS470624,SRA098000,GEO,National University of Singapore,1,0.01773,,0.00917,,0.99646,,0.56398,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-08-15,Adult,Adult,Liver,Liver and Biliary System
37271,SRR1050719,SRX392663,SRS515660,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,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. 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 three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X+M D+,GSM1289483,,source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline,X+M D+,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline,GSM1289483,GSM1289483: X+M D+; Danio rerio; RNA Seq,GSM1289483,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289483,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X+M-D+.csfasta.gz X+M-D+.qual,SOLiD_native SOLiD_native,367532585.0,10500931.0,GSM1289483 r1,0:35,0:113917936;1:90770860;2:74839037;3:87267038;.:737714,35,,,,,,,,,SRX392663,SRS515660,SRA117588,GEO,National University of Singapore,1,0.03142,,0.01041,,0.99115,,0.47722,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37272,SRR1050718,SRX392662,SRS515661,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,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. 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 three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X M+D+,GSM1289482,,source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline,X M+D+,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline,GSM1289482,GSM1289482: X M+D+; Danio rerio; RNA Seq,GSM1289482,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289482,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X-M+D+.csfasta.gz X-M+D+.qual,SOLiD_native SOLiD_native,524940885.0,14998311.0,GSM1289482 r1,0:35,0:177873348;1:126792787;2:107434769;3:111636161;.:1203820,35,,,,,,,,,SRX392662,SRS515661,SRA117588,GEO,National University of Singapore,1,0.04433,,0.02519,,0.99456,,0.5443,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37273,SRR1050717,SRX392661,SRS515658,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,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. 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 three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X M D+,GSM1289481,,source name:control liver|tissue:liver|genotype:wildtype sibling|agent:doxycycline,X M D+,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:wildtype sibling|agent:doxycycline,GSM1289481,GSM1289481: X M D+; Danio rerio; RNA Seq,GSM1289481,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289481,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X-M-D+.csfasta.gz X-M-D+.qual,SOLiD_native SOLiD_native,503677265.0,14390779.0,GSM1289481 r1,0:35,0:153190412;1:124381654;2:106372352;3:118615876;.:1116971,35,,,,,,,,,SRX392661,SRS515658,SRA117588,GEO,National University of Singapore,1,0.03136,,0.01201,,0.99356,,0.49598,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37274,SRR1050716,SRX392660,SRS515659,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,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. 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 three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X+M D ,GSM1289480,,source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1,X+M D ,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1,GSM1289480,GSM1289480: X+M D ; Danio rerio; RNA Seq,GSM1289480,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289480,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X+M-D-.csfasta.gz X+M-D-.qual,SOLiD_native SOLiD_native,634523960.0,18129256.0,GSM1289480 r1,0:35,0:234010528;1:135057441;2:132344184;3:131577105;.:1534702,35,,,,,,,,,SRX392660,SRS515659,SRA117588,GEO,National University of Singapore,1,0.06814,,0.05142,,0.99579,,0.6174,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37275,SRR1050715,SRX392659,SRS515657,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,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. 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 three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X M+D ,GSM1289479,,source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1,X M+D ,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1,GSM1289479,GSM1289479: X M+D ; Danio rerio; RNA Seq,GSM1289479,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289479,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X-M+D-.csfasta.gz X-M+D-.qual,SOLiD_native SOLiD_native,417548565.0,11929959.0,GSM1289479 r1,0:35,0:114209112;1:103552786;2:91302789;3:107590004;.:893874,35,,,,,,,,,SRX392659,SRS515657,SRA117588,GEO,National University of Singapore,1,0.02253,,0.00519,,0.99218,,0.61466,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37276,SRR1050714,SRX392658,SRS515656,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,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. 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 three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X M D ,GSM1289478,,source name:control liver|tissue:liver|genotype:wildtype sibling|agent:n1,X M D ,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:wildtype sibling|agent:n1,GSM1289478,GSM1289478: X M D ; Danio rerio; RNA Seq,GSM1289478,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289478,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X-M-D-.csfasta.gz X-M-D-.qual,SOLiD_native SOLiD_native,522827305.0,14937923.0,GSM1289478 r1,0:35,0:143962506;1:130748449;2:106995057;3:140038917;.:1082376,35,,,,,,,,,SRX392658,SRS515656,SRA117588,GEO,National University of Singapore,1,0.02926,,0.00817,,0.99022,,0.53421,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37277,SRR1057959,SRX398517,SRS518969,SRP034710,PRJNA232516,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE53630,Transcriptome Analysis,The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system,,pubmed:24633177,,6T2,GSM1297515,,source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis,6T2,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor,one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis,GSM1297515,GSM1297515: 6T2; Danio rerio; RNA Seq,GSM1297515,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1297515,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP034710,,,6T2.csfasta.gz 6T2.qual.gz,SOLiD_native SOLiD_native,818910190.0,23397434.0,GSM1297515 r1,0:35,0:347259734;1:164743259;2:162029194;3:130508344;.:14369659,35,,,,,,,,,SRX398517,SRS518969,SRA122333,GEO,National University of Singapore,1,0.03756,,0.0064,,0.99931,,0.92063,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-24,Undetermined,Adult,Liver,Liver and Biliary System
37278,SRR1057958,SRX398516,SRS518968,SRP034710,PRJNA232516,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE53630,Transcriptome Analysis,The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system,,pubmed:24633177,,6T1,GSM1297514,,source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis,6T1,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor,one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis,GSM1297514,GSM1297514: 6T1; Danio rerio; RNA Seq,GSM1297514,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1297514,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP034710,,,6T1.csfasta.gz 6T1.qual.gz,SOLiD_native SOLiD_native,761241005.0,21749743.0,GSM1297514 r1,0:35,0:306840116;1:164725874;2:160786359;3:126370697;.:2517959,35,,,,,,,,,SRX398516,SRS518968,SRA122333,GEO,National University of Singapore,1,0.0542,,0.00664,,0.99876,,0.95184,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-24,Undetermined,Adult,Liver,Liver and Biliary System
37279,SRR1057957,SRX398515,SRS518967,SRP034710,PRJNA232516,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE53630,Transcriptome Analysis,The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system,,pubmed:24633177,,6M2,GSM1297513,,source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control,6M2,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control,GSM1297513,GSM1297513: 6M2; Danio rerio; RNA Seq,GSM1297513,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1297513,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP034710,,,6M2.csfasta.gz 6M2.qual.gz,SOLiD_native SOLiD_native,627546330.0,20918211.0,GSM1297513 r1,0:30,0:265606277;1:113800100;2:158432886;3:89099865;.:607202,30,,,,,,,,,SRX398515,SRS518967,SRA122333,GEO,National University of Singapore,1,0.28369,,0.05854,,0.97611,,0.92541,,30,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-24,Undetermined,Adult,Liver,Liver and Biliary System
37280,SRR1057956,SRX398514,SRS518966,SRP034710,PRJNA232516,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE53630,Transcriptome Analysis,The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system,,pubmed:24633177,,6M1,GSM1297512,,source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control,6M1,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control,GSM1297512,GSM1297512: 6M1; Danio rerio; RNA Seq,GSM1297512,,1,Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1297512,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP034710,,,6M1.csfasta.gz 6M1.qual.gz,SOLiD_native SOLiD_native,670343910.0,22344797.0,GSM1297512 r1,0:30,0:270812672;1:123662771;2:177982653;3:97335698;.:550116,30,,,,,,,,,SRX398514,SRS518966,SRA122333,GEO,National University of Singapore,1,0.28477,,0.05061,,0.9735,,0.86701,,30,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-24,Undetermined,Adult,Liver,Liver and Biliary System
41813,SRR5196073,SRX2511744,SRS1935437,SRP097636,PRJNA362941,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE93965,Transcriptome Analysis,The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma livers of transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.,,pubmed:31827597,,NormM,GSM2465777,,source name:Normal liver of transgenic fishes under mifeprist1|tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,NormM,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample,Normal liver of transgenic fishes under mifepristone,One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water.,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,,tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,GSM2465777,GSM2465777: NormM; Danio rerio; RNA Seq,GSM2465777,,1,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,GEO Accession:GSM2465777,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP097636,,,solid_SAGE3_6M2_F3.csfasta.gz solid_SAGE3_6M2_F3_QV.qual.gz,SOLiD_native SOLiD_native,627546330.0,20918211.0,GSM2465777 r1,0:30,0:265606277;1:113800100;2:158432886;3:89099865;.:607202,30,,,,,,,,,SRX2511744,SRS1935437,SRA530985,GEO,The Biomedical Center,1,0.28369,,0.05854,,0.97605,,0.92502,,30,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2017-01-23,Undetermined,Adult,Liver,Liver and Biliary System
41814,SRR5196072,SRX2511743,SRS1935436,SRP097636,PRJNA362941,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE93965,Transcriptome Analysis,The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma livers of transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.,,pubmed:31827597,,Norm,GSM2465776,,source name:Normal liver of transgenic fishes|tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,Norm,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample,Normal liver of transgenic fishes,One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water.,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,,tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,GSM2465776,GSM2465776: Norm; Danio rerio; RNA Seq,GSM2465776,,1,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,GEO Accession:GSM2465776,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP097636,,,solid_SAGE3_6M1_F3.csfasta.gz solid_SAGE3_6M1_F3_QV.qual.gz,SOLiD_native SOLiD_native,670343910.0,22344797.0,GSM2465776 r1,0:30,0:270812672;1:123662771;2:177982653;3:97335698;.:550116,30,,,,,,,,,SRX2511743,SRS1935436,SRA530985,GEO,The Biomedical Center,1,0.28477,,0.05056,,0.97348,,0.86678,,30,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2017-01-23,Undetermined,Adult,Liver,Liver and Biliary System