{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Larval\" and experiment.platform = \"ABI_SOLID\"", "rows": [[36506, "SRR566696", "SRX185761", "SRS361914", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: liver tumor  M+D+", "GSM1000561: M+D+ 2", "GSM1000561", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "M+D+ 2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor  M+D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "GSM1000561", "GSM1000561: M+D+ 2; Danio rerio; RNA Seq", "GSM1000561 1", null, "1", null, "GEO Accession:GSM1000561", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D+_2_QV.qual M+D+_2.csfasta", "SOLiD_native SOLiD_native", 1493416960.0, 42669056.0, "GSM1000561 r1", "0:35", "0:377247910;1:348861020;2:522134600;3:237405266;.:7768164", 35, null, null, null, null, null, null, null, null, "SRX185761", "SRS361914", "SRA058618", "GEO", "National University of Singapore", 1, 0.06244, null, 0.00306, null, 0.99567, null, 0.34618, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36507, "SRR566695", "SRX185760", "SRS361913", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: liver tumor  M+D+", "GSM1000560: M+D+ 1", "GSM1000560", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "M+D+ 1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor  M+D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "GSM1000560", "GSM1000560: M+D+ 1; Danio rerio; RNA Seq", "GSM1000560 1", null, "1", null, "GEO Accession:GSM1000560", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, null, null, 1291539515.0, 36901129.0, "GSM1000560 r1", "0:35", "0:266006021;1:328523841;2:440474617;3:254266912;.:2268124", 35, null, null, null, null, null, null, null, null, "SRX185760", "SRS361913", "SRA058618", "GEO", "National University of Singapore", 1, 0.10629, null, 0.0044, null, 0.99239, null, 0.31953, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36508, "SRR566694", "SRX185759", "SRS361912", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M D+", "GSM1000559: M D+ 2", "GSM1000559", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "M D+ 2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "GSM1000559", "GSM1000559: M D+ 2; Danio rerio; RNA Seq", "GSM1000559 1", null, "1", null, "GEO Accession:GSM1000559", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D+_2_QV.qual", "SOLiD_native", 1438423910.0, 41097826.0, "GSM1000559 r1", "0:35", "0:353104627;1:349496969;2:433338629;3:275089557;.:27394128", 35, null, null, null, null, null, null, null, null, "SRX185759", "SRS361912", "SRA058618", "GEO", "National University of Singapore", 1, 0.04748, null, 0.00442, null, 0.99425, null, 0.53794, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36509, "SRR566693", "SRX185758", "SRS361911", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M D+", "GSM1000558: M D+ 1", "GSM1000558", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "M D+ 1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "GSM1000558", "GSM1000558: M D+ 1; Danio rerio; RNA Seq", "GSM1000558 1", null, "1", null, "GEO Accession:GSM1000558", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D+_1.csfasta", "SOLiD_native", 1284638285.0, 36703951.0, "GSM1000558 r1", "0:35", "0:328871758;1:317693850;2:402981931;3:233637468;.:1453278", 35, null, null, null, null, null, null, null, null, "SRX185758", "SRS361911", "SRA058618", "GEO", "National University of Singapore", 1, 0.10539, null, 0.00562, null, 0.99141, null, 0.37635, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36510, "SRR566692", "SRX185757", "SRS361910", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M+D ", "GSM1000557: M+D  2", "GSM1000557", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "M+D  2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M+D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "GSM1000557", "GSM1000557: M+D  2; Danio rerio; RNA Seq", "GSM1000557 1", null, "1", null, "GEO Accession:GSM1000557", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D-_2_QV.qual", "SOLiD_native", 1404966080.0, 40141888.0, "GSM1000557 r1", "0:35", "0:371691603;1:354481639;2:405221861;3:271978812;.:1592165", 35, null, null, null, null, null, null, null, null, "SRX185757", "SRS361910", "SRA058618", "GEO", "National University of Singapore", 1, 0.07869, null, 0.00455, null, 0.99253, null, 0.51508, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36511, "SRR566691", "SRX185756", "SRS361909", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M+D ", "GSM1000556: M+D  1", "GSM1000556", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "M+D  1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M+D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "GSM1000556", "GSM1000556: M+D  1; Danio rerio; RNA Seq", "GSM1000556 1", null, "1", null, "GEO Accession:GSM1000556", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D-_1_QV.qual M+D-_1.csfasta", "SOLiD_native SOLiD_native", 1286706820.0, 36763052.0, "GSM1000556 r1", "0:35", "0:252864341;1:338709089;2:436928155;3:256235022;.:1970213", 35, null, null, null, null, null, null, null, null, "SRX185756", "SRS361909", "SRA058618", "GEO", "National University of Singapore", 1, 0.12399, null, 0.00617, null, 0.98752, null, 0.50351, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36512, "SRR566690", "SRX185755", "SRS361908", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M D ", "GSM1000555: M D  2", "GSM1000555", null, "genotype:wildtype|tissue:liver|treatment:n1", "M D  2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:n1", "GSM1000555", "GSM1000555: M D  2; Danio rerio; RNA Seq", "GSM1000555 1", null, "1", null, "GEO Accession:GSM1000555", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D-_2_QV.qual M-D-_2.csfasta", "SOLiD_native SOLiD_native", 1337952770.0, 38227222.0, "GSM1000555 r1", "0:35", "0:391863829;1:347720340;2:312814682;3:283542736;.:2011183", 35, null, null, null, null, null, null, null, null, "SRX185755", "SRS361908", "SRA058618", "GEO", "National University of Singapore", 1, 0.04605, null, 0.00365, null, 0.99494, null, 0.51825, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36513, "SRR566689", "SRX185754", "SRS361907", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M D ", "GSM1000554: M D  1", "GSM1000554", null, "genotype:wildtype|tissue:liver|treatment:n1", "M D  1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:n1", "GSM1000554", "GSM1000554: M D  1; Danio rerio; RNA Seq", "GSM1000554 1", null, "1", null, "GEO Accession:GSM1000554", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D-_1.csfasta", "SOLiD_native", 1395143680.0, 39861248.0, "GSM1000554 r1", "0:35", "0:439852883;1:355203725;2:298639546;3:299770820;.:1676706", 35, null, null, null, null, null, null, null, null, "SRX185754", "SRS361907", "SRA058618", "GEO", "National University of Singapore", 1, 0.02094, null, 0.00123, null, 0.99784, null, 0.58426, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36685, "SRR801688", "SRX258168", "SRS406299", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish 1 wpf larvae", "GSM1112163: larva  1 week", "GSM1112163", null, "strain:AB|developmental stage:larva  1 week|tissue:larva", "larva  1 week", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish 1 wpf larvae", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:larva  1 week|tissue:larva", "GSM1112163", "GSM1112163: larva  1 week; Danio rerio; RNA Seq", "GSM1112163 1", null, "1", null, "GEO Accession:GSM1112163", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_1week_F3.csfasta.bz2 D_rerio_1week_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 18866346300.0, 377326926.0, "GSM1112163 r1", "0:50", "0:4319577052;1:5210931849;2:5202393345;3:4013865803;.:119578251", 50, null, null, null, null, null, null, null, null, "SRX258168", "SRS406299", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.60649, null, 0.05524, null, 0.86746, null, 0.51092, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [36686, "SRR801687", "SRX258167", "SRS406298", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish embryos at the Protruding mouth stage", "GSM1112162: Protruding mouth  72hpf", "GSM1112162", null, "strain:AB|developmental stage:Protruding mouth  72hpf|tissue:embryo", "Protruding mouth  72hpf", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish embryos at the Protruding mouth stage", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:Protruding mouth  72hpf|tissue:embryo", "GSM1112162", "GSM1112162: Protruding mouth  72hpf; Danio rerio; RNA Seq", "GSM1112162 1", null, "1", null, "GEO Accession:GSM1112162", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_72hpf_F3.csfasta.bz2 D_rerio_72hpf_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 19339397750.0, 386787955.0, "GSM1112162 r1", "0:50", "0:4755453154;1:5011845177;2:5110574744;3:4002085043;.:459439632", 50, null, null, null, null, null, null, null, null, "SRX258167", "SRS406298", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.34099, null, 0.03045, null, 0.92409, null, 0.49783, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [37907, "SRR1104969", "SRX424037", "SRS527958", "SRP035264", "PRJNA236557", "Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq]", "GSE53758", "Transcriptome Analysis", "To determine the global impact of the clbn mutation on gene expression and efficiency of U2  and U12 type splicing  we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each  genotyped homozygous wildtype and homozygous clbns841 mutants  respectively", "parent bioproject:PRJNA236230", "pubmed:24516132", null, "108hpf clbn", "GSM1303831", null, "source name:108hpf clbn larvae|genotype/variation:clbns841|development stage:108 hpf|tissue:whole larvae", "108hpf clbn", "50bp single end reads were mapped  using the X MATE recursive mapping pipeline 42  allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis  RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis  RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9", "108hpf clbn larvae", "Starting at 24 hpf  embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation", "Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first  and aqueous phases of all homozygous wildtype and mutant larvae  respectively  were pooled prior to RNA precipiation with isopropanol. For RNA sequencing  RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide  8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.", "Embryos for all experiments were produced by natural spawning  transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5\u00b0C incubator on a 12h light/dark cycle.", "genotype/variation:clbns841|developmental stage:108 hpf|tissue:whole larvae", "GSM1303831", "GSM1303831: 108hpf clbn; Danio rerio; RNA Seq", "GSM1303831", null, "1", "Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first  and aqueous phases of all homozygous wildtype and mutant larvae  respectively  were pooled prior to RNA precipiation with isopropanol. For RNA sequencing  RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide  8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.", "GEO Accession:GSM1303831", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP035264", null, null, "108hpf_clbn_F3_QV.qual.bz2 108hpf_clbn_F3.csfasta.bz2", "SOLiD_native SOLiD_native", 2698882700.0, 53977654.0, "GSM1303831 r1", "0:50", "0:653022205;1:711705790;2:753066133;3:571973990;.:9114582", 50, null, null, null, null, null, null, null, null, "SRX424037", "SRS527958", "SRA123959", "GEO", "Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research", 1, 0.56134, null, 0.05842, null, 0.84303, null, 0.49093, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2014-01-09", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [37908, "SRR1104968", "SRX424036", "SRS527957", "SRP035264", "PRJNA236557", "Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq]", "GSE53758", "Transcriptome Analysis", "To determine the global impact of the clbn mutation on gene expression and efficiency of U2  and U12 type splicing  we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each  genotyped homozygous wildtype and homozygous clbns841 mutants  respectively", "parent bioproject:PRJNA236230", "pubmed:24516132", null, "108hpf wt", "GSM1303830", null, "source name:108hpf wt larvae|genotype/variation:wildtype|development stage:108 hpf|tissue:whole larvae", "108hpf wt", "50bp single end reads were mapped  using the X MATE recursive mapping pipeline 42  allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis  RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis  RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9", "108hpf wt larvae", "Starting at 24 hpf  embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation", "Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first  and aqueous phases of all homozygous wildtype and mutant larvae  respectively  were pooled prior to RNA precipiation with isopropanol. For RNA sequencing  RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide  8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.", "Embryos for all experiments were produced by natural spawning  transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5\u00b0C incubator on a 12h light/dark cycle.", "genotype/variation:wildtype|developmental stage:108 hpf|tissue:whole larvae", "GSM1303830", "GSM1303830: 108hpf wt; Danio rerio; RNA Seq", "GSM1303830", null, "1", "Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first  and aqueous phases of all homozygous wildtype and mutant larvae  respectively  were pooled prior to RNA precipiation with isopropanol. For RNA sequencing  RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide  8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.", "GEO Accession:GSM1303830", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP035264", null, null, "108hpf_wt_F3_QV.qual.bz2 108hpf_wt_F3.csfasta.bz2", "SOLiD_native SOLiD_native", 2835473700.0, 56709474.0, "GSM1303830 r1", "0:50", "0:697915785;1:748317376;2:781024795;3:605838541;.:2377203", 50, null, null, null, null, null, null, null, null, "SRX424036", "SRS527957", "SRA123959", "GEO", "Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research", 1, 0.57033, null, 0.05759, null, 0.8384, null, 0.49692, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2014-01-09", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 12, "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": "Larval", "p1": "ABI_SOLID"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&experiment.platform=ABI_SOLID", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&experiment.platform=ABI_SOLID&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", 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