{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Adult\" and experiment.platform = \"ABI_SOLID\"", "rows": [[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.", null, "pubmed:24176670;pubmed:23922661", null, "H2O treated zebrafish liver", "GSM1177837", null, "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.", null, "genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control", "GSM1177837", "GSM1177837: H2O treated zebrafish liver; Danio rerio; RNA Seq", "GSM1177837", null, "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", null, "SRP026400", null, null, "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, null, null, null, null, null, null, null, null, "SRX316721", "SRS472258", "SRA091803", "GEO", "National University of Singapore", 1, 0.02019, null, 0.01385, null, 0.9973, null, 0.64062, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:24176670;pubmed:23922661", null, "Arsenic treated zebrafish liver", "GSM1177836", null, "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.", null, "genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium", "GSM1177836", "GSM1177836: Arsenic treated zebrafish liver; Danio rerio; RNA Seq", "GSM1177836", null, "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", null, "SRP026400", null, null, "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, null, null, null, null, null, null, null, null, "SRX316720", "SRS454027", "SRA091803", "GEO", "National University of Singapore", 1, 0.0161, null, 0.00302, null, 0.99334, null, 0.51629, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24204792", null, "DMSO", "GSM1209643", null, "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.", null, "tissue:liver|genotype:wildtype sibling|treatment:DMSO", "GSM1209643", "GSM1209643: DMSO; Danio rerio; RNA Seq", "GSM1209643", null, "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", null, "SRP028848", null, null, "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, null, null, null, null, null, null, null, null, "SRX335554", "SRS470625", "SRA098000", "GEO", "National University of Singapore", 1, 0.01735, null, 0.00647, null, 0.9946, null, 0.51324, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24204792", null, "TCDD", "GSM1209642", null, "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.", null, "tissue:liver|genotype:wildtype sibling|treatment:TCDD", "GSM1209642", "GSM1209642: TCDD; Danio rerio; RNA Seq", "GSM1209642", null, "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", null, "SRP028848", null, null, "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, null, null, null, null, null, null, null, null, "SRX335553", "SRS470624", "SRA098000", "GEO", "National University of Singapore", 1, 0.01773, null, 0.00917, null, 0.99646, null, 0.56398, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "X+M D+", "GSM1289483", null, "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.", null, "tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline", "GSM1289483", "GSM1289483: X+M D+; Danio rerio; RNA Seq", "GSM1289483", 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:GSM1289483", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "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, null, null, null, null, null, null, null, null, "SRX392663", "SRS515660", "SRA117588", "GEO", "National University of Singapore", 1, 0.03142, null, 0.01041, null, 0.99115, null, 0.47722, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "X M+D+", "GSM1289482", null, "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.", null, "tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline", "GSM1289482", "GSM1289482: X M+D+; Danio rerio; RNA Seq", "GSM1289482", 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:GSM1289482", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "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, null, null, null, null, null, null, null, null, "SRX392662", "SRS515661", "SRA117588", "GEO", "National University of Singapore", 1, 0.04433, null, 0.02519, null, 0.99456, null, 0.5443, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "X M D+", "GSM1289481", null, "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.", null, "tissue:liver|genotype:wildtype sibling|agent:doxycycline", "GSM1289481", "GSM1289481: X M D+; Danio rerio; RNA Seq", "GSM1289481", 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:GSM1289481", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "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, null, null, null, null, null, null, null, null, "SRX392661", "SRS515658", "SRA117588", "GEO", "National University of Singapore", 1, 0.03136, null, 0.01201, null, 0.99356, null, 0.49598, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "X+M D ", "GSM1289480", null, "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.", null, "tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1", "GSM1289480", "GSM1289480: X+M D ; Danio rerio; RNA Seq", "GSM1289480", 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:GSM1289480", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "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, null, null, null, null, null, null, null, null, "SRX392660", "SRS515659", "SRA117588", "GEO", "National University of Singapore", 1, 0.06814, null, 0.05142, null, 0.99579, null, 0.6174, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "X M+D ", "GSM1289479", null, "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.", null, "tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1", "GSM1289479", "GSM1289479: X M+D ; Danio rerio; RNA Seq", "GSM1289479", 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:GSM1289479", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "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, null, null, null, null, null, null, null, null, "SRX392659", "SRS515657", "SRA117588", "GEO", "National University of Singapore", 1, 0.02253, null, 0.00519, null, 0.99218, null, 0.61466, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "X M D ", "GSM1289478", null, "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.", null, "tissue:liver|genotype:wildtype sibling|agent:n1", "GSM1289478", "GSM1289478: X M D ; Danio rerio; RNA Seq", "GSM1289478", 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:GSM1289478", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "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, null, null, null, null, null, null, null, null, "SRX392658", "SRS515656", "SRA117588", "GEO", "National University of Singapore", 1, 0.02926, null, 0.00817, null, 0.99022, null, 0.53421, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48021, "SRR6915090", "SRX3862779", "SRS3104834", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "10dpa replicate3", "GSM3071386", null, "source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "10dpa replicate3", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 10 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071386", "GSM3071386: 10dpa replicate3; Danio rerio; RNA Seq", "GSM3071386", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071386", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L03-1-Idx_10-10.bam", "bam", 682375516.0, 14088728.0, "GSM3071386 r1", "0:48.43", "A:140419665;C:148759068;G:176799261;T:168695522;N:47702000", 48, null, null, null, 140419665, 148759068, 176799261, 168695522, 47702000, "SRX3862779", "SRS3104834", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.76603, null, 0.04459, null, 0.79752, null, 0.50424, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48022, "SRR6915089", "SRX3862778", "SRS3104833", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "3dpa replicate3", "GSM3071385", null, "source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "3dpa replicate3", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 3 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071385", "GSM3071385: 3dpa replicate3; Danio rerio; RNA Seq", "GSM3071385", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071385", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L03-1-Idx_12-12.bam", "bam", 901887293.0, 18522789.0, "GSM3071385 r1", "0:48.69", "A:184300673;C:193849264;G:243428119;T:224471972;N:55837265", 48, null, null, null, 184300673, 193849264, 243428119, 224471972, 55837265, "SRX3862778", "SRS3104833", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.78632, null, 0.03154, null, 0.79707, null, 0.51779, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48023, "SRR6915088", "SRX3862777", "SRS3104832", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "2dpa replicate3", "GSM3071384", null, "source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "2dpa replicate3", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 2 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071384", "GSM3071384: 2dpa replicate3; Danio rerio; RNA Seq", "GSM3071384", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071384", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L03-1-Idx_11-11.bam", "bam", 850810410.0, 17462158.0, "GSM3071384 r1", "0:48.72", "A:176186499;C:182052044;G:228063922;T:213571294;N:50936651", 48, null, null, null, 176186499, 182052044, 228063922, 213571294, 50936651, "SRX3862777", "SRS3104832", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.77804, null, 0.03462, null, 0.80229, null, 0.49822, null, 43, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48024, "SRR6915087", "SRX3862776", "SRS3104831", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "0dpa replicate3", "GSM3071383", null, "source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "0dpa replicate3", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 0 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071383", "GSM3071383: 0dpa replicate3; Danio rerio; RNA Seq", "GSM3071383", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071383", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L03-1-Idx_9-9.bam", "bam", 598710241.0, 12328728.0, "GSM3071383 r1", "0:48.56", "A:121889198;C:129444719;G:158430979;T:150128070;N:38817275", 48, null, null, null, 121889198, 129444719, 158430979, 150128070, 38817275, "SRX3862776", "SRS3104831", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.77, null, 0.03334, null, 0.799, null, 0.45925, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48025, "SRR6915086", "SRX3862775", "SRS3104830", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "10dpa replicate2", "GSM3071382", null, "source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "10dpa replicate2", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 10 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071382", "GSM3071382: 10dpa replicate2; Danio rerio; RNA Seq", "GSM3071382", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071382", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L02-1-Idx_8-8.bam", "bam", 1205021238.0, 24639106.0, "GSM3071382 r1", "0:48.91", "A:255022070;C:275793907;G:309172527;T:294800027;N:70232707", 48, null, null, null, 255022070, 275793907, 309172527, 294800027, 70232707, "SRX3862775", "SRS3104830", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.80398, null, 0.05829, null, 0.78644, null, 0.4993, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48026, "SRR6915085", "SRX3862774", "SRS3104829", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "3dpa replicate2", "GSM3071381", null, "source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "3dpa replicate2", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 3 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071381", "GSM3071381: 3dpa replicate2; Danio rerio; RNA Seq", "GSM3071381", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071381", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L02-1-Idx_10-10.bam", "bam", 1479531813.0, 30219937.0, "GSM3071381 r1", "0:48.96", "A:314793261;C:331769330;G:384109921;T:369987947;N:78871354", 48, null, null, null, 314793261, 331769330, 384109921, 369987947, 78871354, "SRX3862774", "SRS3104829", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.81777, null, 0.03195, null, 0.7821, null, 0.49263, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48027, "SRR6915084", "SRX3862773", "SRS3104828", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "2dpa replicate2", "GSM3071380", null, "source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "2dpa replicate2", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 2 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071380", "GSM3071380: 2dpa replicate2; Danio rerio; RNA Seq", "GSM3071380", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071380", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L02-1-Idx_9-9.bam", "bam", 834856811.0, 17079585.0, "GSM3071380 r1", "0:48.88", "A:179851654;C:186667201;G:209784080;T:212166083;N:46387793", 48, null, null, null, 179851654, 186667201, 209784080, 212166083, 46387793, "SRX3862773", "SRS3104828", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.80341, null, 0.02786, null, 0.78031, null, 0.49876, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48028, "SRR6915083", "SRX3862772", "SRS3104827", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "0dpa replicate2", "GSM3071379", null, "source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "0dpa replicate2", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 0 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071379", "GSM3071379: 0dpa replicate2; Danio rerio; RNA Seq", "GSM3071379", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071379", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L02-1-Idx_7-7.bam", "bam", 821645371.0, 16824250.0, "GSM3071379 r1", "0:48.84", "A:169383232;C:176200663;G:223364159;T:207905438;N:44791879", 48, null, null, null, 169383232, 176200663, 223364159, 207905438, 44791879, "SRX3862772", "SRS3104827", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.79697, null, 0.04152, null, 0.79513, null, 0.48078, null, 34, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48029, "SRR6915082", "SRX3862771", "SRS3104826", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "10dpa replicate1", "GSM3071378", null, "source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "10dpa replicate1", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 10 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071378", "GSM3071378: 10dpa replicate1; Danio rerio; RNA Seq", "GSM3071378", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071378", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L01-1-Idx_4-4.bam", "bam", 1056921416.0, 21553661.0, "GSM3071378 r1", "0:49.04", "A:223138065;C:233998717;G:286278215;T:261736901;N:51769518", 49, null, null, null, 223138065, 233998717, 286278215, 261736901, 51769518, "SRX3862771", "SRS3104826", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.81372, null, 0.06015, null, 0.79017, null, 0.49818, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48030, "SRR6915081", "SRX3862770", "SRS3104824", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "3dpa replicate1", "GSM3071377", null, "source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "3dpa replicate1", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 3 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071377", "GSM3071377: 3dpa replicate1; Danio rerio; RNA Seq", "GSM3071377", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071377", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L01-1-Idx_6-6.bam", "bam", 614372216.0, 12531168.0, "GSM3071377 r1", "0:49.03", "A:129828689;C:133826356;G:168985348;T:153858339;N:27873484", 49, null, null, null, 129828689, 133826356, 168985348, 153858339, 27873484, "SRX3862770", "SRS3104824", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.81659, null, 0.02803, null, 0.78987, null, 0.49295, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48031, "SRR6915080", "SRX3862769", "SRS3104825", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "2dpa replicate1", "GSM3071376", null, "source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "2dpa replicate1", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 2 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071376", "GSM3071376: 2dpa replicate1; Danio rerio; RNA Seq", "GSM3071376", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071376", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L01-1-Idx_5-5.bam", "bam", 1317408760.0, 26870813.0, "GSM3071376 r1", "0:49.03", "A:278980295;C:285236037;G:357022664;T:334390621;N:61779143", 49, null, null, null, 278980295, 285236037, 357022664, 334390621, 61779143, "SRX3862769", "SRS3104825", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.81546, null, 0.02559, null, 0.79328, null, 0.48857, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"], [48032, "SRR6915079", "SRX3862768", "SRS3104823", "SRP136710", "PRJNA447984", "RNA seq data from adult zebrafish caudal fin regeneration", "GSE112498", "Transcriptome Analysis", "Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.", null, "pubmed:30031067", null, "0dpa replicate1", "GSM3071375", null, "source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "0dpa replicate1", "SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample", "caudal fin tissue 0 dy post amputation", "Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80\u00b0C before RNA extraction.", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "Adult fish were raised at 28\u00b0C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.", "tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf", "GSM3071375", "GSM3071375: 0dpa replicate1; Danio rerio; RNA Seq", "GSM3071375", null, "1", "RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.", "GEO Accession:GSM3071375", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB 5500 Genetic Analyzer", null, "SRP136710", null, "options:  accept hard clip", "Solid5500_2014_11_07_1_L01-1-Idx_3-3.bam", "bam", 975324708.0, 19881338.0, "GSM3071375 r1", "0:49.06", "A:203549346;C:215407985;G:265949502;T:244027187;N:46390688", 49, null, null, null, 203549346, 215407985, 265949502, 244027187, 46390688, "SRX3862768", "SRS3104823", "SRA676352", "GEO", "Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon", 1, 0.80817, null, 0.05047, null, 0.79569, null, 0.47149, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "France", "2018-03-29", "Adult", "Adult", "Fin", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 22, 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"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": "Adult", "p1": "ABI_SOLID"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&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": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "cDNA", "label": "cDNA", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "ABI_SOLID", "label": "ABI_SOLID", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "Adult", "label": "Adult", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&devstage_curation_coarse=Adult", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "Adult", "label": "Adult", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ABI_SOLID", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "Surface Structure", "label": "Surface Structure", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&tissue_curation_coarse=Surface+Structure", "selected": false}, {"value": "Liver and Biliary System", "label": "Liver and Biliary System", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&tissue_curation_coarse=Liver+and+Biliary+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "Fin", "label": "Fin", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&tissue_curation=Fin", "selected": false}, {"value": "Liver", "label": "Liver", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&tissue_curation=Liver", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID", "results": [{"value": "unknown", "label": "unknown", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Adult&experiment.platform=ABI_SOLID&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 99.31994900398422}