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Overall design: Examination of mRNA levels in individual line at three month of age.", null, null, null, "mRNA from HBx transgenic line", "GSM850199", null, "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 \u00b0C.", "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", null, "GEO Accession:GSM850199", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009863", null, null, "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, null, null, null, null, null, null, null, null, "SRX112003", "SRS282724", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.70675, null, 0.04174, null, 0.94146, null, 0.22954, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "mRNA from AB strain", "GSM850198", null, "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 \u00b0C.", "phenotype:n1|strain:AB|tissue:liver", "GSM850198", "GSM850198: mRNA from AB strain; Danio rerio; RNA Seq", "GSM850198 1", "GSM850198: mRNA from AB strain", "1", null, "GEO Accession:GSM850198", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009863", null, null, "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, null, null, null, null, null, null, null, null, "SRX112002", "SRS282723", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.73072, null, 0.04843, null, 0.95574, null, 0.21796, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Taiwan", "2011-12-16", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [36739, "SRR867022", "SRX286270", "SRS420566", "SRP022549", "PRJNA202401", "Danio rerio Transcriptome or Gene expression", "PRJNA202401", "Other", "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.", null, null, "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish", "General Sample for Danio rerio", "ICH", null, "strain:wild type", null, null, null, null, null, null, null, null, "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  Bcat", "Danio rerio boot", "1", "RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. 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Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP022549", null, null, "s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual", "SOLiD_native SOLiD_native", 10810535400.0, 216210708.0, "Zebrafish DV patterning ICH", "0:50", "0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417", 50, null, null, null, null, null, null, null, null, "SRX286271", "SRS420566", "SRA075737", "BAYGEN|NGSP", "BAYGEN", 1, 0.42474, null, 0.06136, null, 0.93434, null, 0.75757, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "3prime", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2013-05-23", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [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. 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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.", null, "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", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. 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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.", null, "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", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. 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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.", null, "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", null, "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", null, "SRP034710", null, null, "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, null, null, null, null, null, null, null, null, "SRX398515", "SRS518967", "SRA122333", "GEO", "National University of Singapore", 1, 0.28369, null, 0.05854, null, 0.97611, null, 0.92541, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "6M1", "GSM1297512", null, "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.", null, "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", null, "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", null, "SRP034710", null, null, "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, null, null, null, null, null, null, null, null, "SRX398514", "SRS518966", "SRA122333", "GEO", "National University of Singapore", 1, 0.28477, null, 0.05061, null, 0.9735, null, 0.86701, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-24", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [41811, "SRR5196075", "SRX2511746", "SRS1935439", "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 2\u00b5M 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.", null, "pubmed:31827597", null, "CarcinomaM", "GSM2465779", null, "source name:Hepatocellular carcinoma of transgenic fishes post mifeprist1 withdrawal|tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line", "CarcinomaM", "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", "Hepatocellular carcinoma of transgenic fishes post mifepristone withdrawal", "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", null, "tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line", "GSM2465779", "GSM2465779: CarcinomaM; Danio rerio; RNA Seq", "GSM2465779", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", "GEO Accession:GSM2465779", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP097636", null, null, "solid_SAGE_6T2_F3.csfasta.gz solid_SAGE_6T2_F3_QV.qual.gz", "SOLiD_native SOLiD_native", 818910190.0, 23397434.0, "GSM2465779 r1", "0:35", "0:347259734;1:164743259;2:162029194;3:130508344;.:14369659", 35, null, null, null, null, null, null, null, null, "SRX2511746", "SRS1935439", "SRA530985", "GEO", "The Biomedical Center", 1, 0.03756, null, 0.00615, null, 0.99928, null, 0.91338, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2017-01-23", "Undetermined", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [41812, "SRR5196074", "SRX2511745", "SRS1935438", "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 2\u00b5M 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.", null, "pubmed:31827597", null, "Carcinoma", "GSM2465778", null, "source name:Hepatocellular carcinoma of transgenic fishes|tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line", "Carcinoma", "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", "Hepatocellular carcinoma 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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", null, "tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line", "GSM2465778", "GSM2465778: Carcinoma; Danio rerio; RNA Seq", "GSM2465778", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", "GEO Accession:GSM2465778", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP097636", null, null, "solid_SAGE_6T1_F3.csfasta.gz solid_SAGE_6T1_F3_QV.qual.gz", "SOLiD_native SOLiD_native", 761241005.0, 21749743.0, "GSM2465778 r1", "0:35", "0:306840116;1:164725874;2:160786359;3:126370697;.:2517959", 35, null, null, null, null, null, null, null, null, "SRX2511745", "SRS1935438", "SRA530985", "GEO", "The Biomedical Center", 1, 0.0543, null, 0.00668, null, 0.9988, null, 0.95092, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2017-01-23", "Undetermined", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 2\u00b5M 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.", null, "pubmed:31827597", null, "NormM", "GSM2465777", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", null, "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", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", "GEO Accession:GSM2465777", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP097636", null, null, "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, null, null, null, null, null, null, null, null, "SRX2511744", "SRS1935437", "SRA530985", "GEO", "The Biomedical Center", 1, 0.28369, null, 0.05854, null, 0.97605, null, 0.92502, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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 2\u00b5M 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.", null, "pubmed:31827597", null, "Norm", "GSM2465776", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", null, "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", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", "GEO Accession:GSM2465776", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP097636", null, null, "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, null, null, null, null, null, null, null, null, "SRX2511743", "SRS1935436", "SRA530985", "GEO", "The Biomedical Center", 1, 0.28477, null, 0.05056, null, 0.97348, null, 0.86678, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2017-01-23", "Undetermined", "Adult", "Liver", "Liver and Biliary System"]], "truncated": false, "filtered_table_rows_count": 14, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Undetermined", "p1": "ABI_SOLID"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&experiment.platform=ABI_SOLID", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 14, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&experiment.platform=ABI_SOLID&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": 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