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
36586,SRR1562528,SRX204106,SRS373224,SRP017135,PRJNA179237,Danio rerio strain:SAT Transcriptome or Gene expression,PRJNA179237,Other,Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.,,,Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas,Zebrafish trancriptome for protegenomic analysis,zebrafish IOB JHU transcriptome,,,,,,,,,,,Zebrafish transcriptome profiling for proteogenomic analysis,JHU IOB zebrafish RNA Seq,1,SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiScanSQ,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017135,,,,,3901027000.0,41246200.0,zebrafish data1,0:50 1:50,A:1065764997;C:896043530;G:867105444;T:1071973870;N:139159,50,50,,,1065764997,896043530,867105444,1071973870,139159,SRX204106,SRS373224,SRA060234,Johns Hopkins University|Pandey Lab,Johns Hopkins University,2,0.95204,0.94561,0.11416,0.11357,0.68235,0.68387,0.47537,0.47688,50,50,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-07-22,Undetermined,Undetermined,Multi-tissue,Multi-system
36587,SRR1562529,SRX204106,SRS373224,SRP017135,PRJNA179237,Danio rerio strain:SAT Transcriptome or Gene expression,PRJNA179237,Other,Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.,,,Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas,Zebrafish trancriptome for protegenomic analysis,zebrafish IOB JHU transcriptome,,,,,,,,,,,Zebrafish transcriptome profiling for proteogenomic analysis,JHU IOB zebrafish RNA Seq,1,SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiScanSQ,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017135,,,,,3298508150.0,34528793.0,zebrafish data2,0:50 1:50,A:870578872;C:780299206;G:764413584;T:883098619;N:117869,50,50,,,870578872,780299206,764413584,883098619,117869,SRX204106,SRS373224,SRA060234,Johns Hopkins University|Pandey Lab,Johns Hopkins University,2,0.96195,0.9525,0.05344,0.0528,0.77285,0.7737,0.44453,0.43789,50,50,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-07-22,Undetermined,Undetermined,Multi-tissue,Multi-system
36588,SRR1562530,SRX204106,SRS373224,SRP017135,PRJNA179237,Danio rerio strain:SAT Transcriptome or Gene expression,PRJNA179237,Other,Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.,,,Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas,Zebrafish trancriptome for protegenomic analysis,zebrafish IOB JHU transcriptome,,,,,,,,,,,Zebrafish transcriptome profiling for proteogenomic analysis,JHU IOB zebrafish RNA Seq,1,SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiScanSQ,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017135,,,,,5033866800.0,52047991.0,zebrafish data6,0:50 1:50,A:1318991279;C:1193979085;G:1179037925;T:1341674073;N:184438,50,50,,,1318991279,1193979085,1179037925,1341674073,184438,SRX204106,SRS373224,SRA060234,Johns Hopkins University|Pandey Lab,Johns Hopkins University,2,0.97568,0.97028,0.03448,0.03488,0.88767,0.88785,0.17745,0.18337,50,50,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-07-22,Undetermined,Undetermined,Multi-tissue,Multi-system
36589,SRR1562531,SRX204106,SRS373224,SRP017135,PRJNA179237,Danio rerio strain:SAT Transcriptome or Gene expression,PRJNA179237,Other,Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.,,,Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas,Zebrafish trancriptome for protegenomic analysis,zebrafish IOB JHU transcriptome,,,,,,,,,,,Zebrafish transcriptome profiling for proteogenomic analysis,JHU IOB zebrafish RNA Seq,1,SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiScanSQ,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017135,,,,,4394828000.0,45714707.0,zebrafish data3,0:50 1:50,A:1146792341;C:1067826128;G:1033443384;T:1146608253;N:157894,50,50,,,1146792341,1067826128,1033443384,1146608253,157894,SRX204106,SRS373224,SRA060234,Johns Hopkins University|Pandey Lab,Johns Hopkins University,2,0.96496,0.95999,0.03952,0.03946,0.78571,0.78518,0.51359,0.49202,50,50,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-07-22,Undetermined,Undetermined,Multi-tissue,Multi-system
36590,SRR1562532,SRX204106,SRS373224,SRP017135,PRJNA179237,Danio rerio strain:SAT Transcriptome or Gene expression,PRJNA179237,Other,Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.,,,Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas,Zebrafish trancriptome for protegenomic analysis,zebrafish IOB JHU transcriptome,,,,,,,,,,,Zebrafish transcriptome profiling for proteogenomic analysis,JHU IOB zebrafish RNA Seq,1,SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiScanSQ,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017135,,,,,3637203400.0,38182310.0,zebrafish data4,0:50 1:50,A:956604323;C:863740756;G:843429871;T:973297634;N:130816,50,50,,,956604323,863740756,843429871,973297634,130816,SRX204106,SRS373224,SRA060234,Johns Hopkins University|Pandey Lab,Johns Hopkins University,2,0.95377,0.94653,0.0656,0.06507,0.72448,0.72541,0.4157,0.41707,50,50,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-07-22,Undetermined,Undetermined,Multi-tissue,Multi-system
36591,SRR1562533,SRX204106,SRS373224,SRP017135,PRJNA179237,Danio rerio strain:SAT Transcriptome or Gene expression,PRJNA179237,Other,Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.,,,Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas,Zebrafish trancriptome for protegenomic analysis,zebrafish IOB JHU transcriptome,,,,,,,,,,,Zebrafish transcriptome profiling for proteogenomic analysis,JHU IOB zebrafish RNA Seq,1,SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiScanSQ,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017135,,,,,4185424200.0,44832788.0,zebrafish data5,0:50 1:50,A:1143949920;C:959926497;G:921201865;T:1160194111;N:151807,50,50,,,1143949920,959926497,921201865,1160194111,151807,SRX204106,SRS373224,SRA060234,Johns Hopkins University|Pandey Lab,Johns Hopkins University,2,0.95163,0.94301,0.12015,0.11974,0.64396,0.64514,0.49698,0.49883,50,50,B,B,biological fallback assumption,illumina,early_illumina,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-07-22,Undetermined,Undetermined,Multi-tissue,Multi-system
36739,SRR867022,SRX286270,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  Bcat,Danio rerio boot,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP022549,,,s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta,SOLiD_native SOLiD_native,9801985250.0,196039705.0,Zebrafish DV patterning Boot,0:50,0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939,50,,,,,,,,,SRX286270,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.59289,,0.09435,,0.92669,,0.7658,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
36740,SRR867023,SRX286271,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  ICH,Danio rerio ICH,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP022549,,,s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual,SOLiD_native SOLiD_native,10810535400.0,216210708.0,Zebrafish DV patterning ICH,0:50,0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417,50,,,,,,,,,SRX286271,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.42474,,0.06136,,0.93434,,0.75757,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined