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
36494,SRR535986,SRX175096,SRS353009,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data nhslMUT was created from 8 pooled nhsl1bfh131 fish that were the siblings of nhslWT.,Miller nhslMUT.bam,Miller nhslMUT.bam,,,,,,,,,,,Miller nhslMUT.bam,Miller nhslMUT.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,fh131MUT.bam,bam,1826508618.0,18449582.0,Miller nhslMUT.bam,0:99,A:483532536;C:434813089;G:419760061;T:488362447;N:40485,99,,,,483532536,434813089,419760061,488362447,40485,SRX175096,SRS353009,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,1,0.98575,,0.08593,,0.71001,,0.48782,,99,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36495,SRR535978,SRX175077,SRS353008,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data nhslWT was created from 8 pooled wildtype fish that were the siblings nhsl1bfh131 mutants nhslMUT.,Miller nhslWT.bam,Miller nhslWT.bam,,,,,,,,,,,Miller nhslWT.bam,Miller nhslWT.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,fh131WT.bam,bam,3473158887.0,35082413.0,Miller nhslWT.bam,0:99,A:938335920;C:812249868;G:790639478;T:931852781;N:80840,99,,,,938335920,812249868,790639478,931852781,80840,SRX175077,SRS353008,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,1,0.98331,,0.07541,,0.71401,,0.47828,,99,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36496,SRR535943,SRX175054,SRS353007,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data vanglMUT was created from 37 pooled vangl2m209 fish that were the siblings of vanglWT.,Miller vanglMUT.bam,Miller vanglMUT.bam,,,,,,,,,,,Miller vanglMUT.bam,Miller vanglMUT.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,VanglMUT.bam,bam,2841728834.0,30417920.0,Miller vanglMUT.bam,0:49 1:49,A:717580081;C:706848901;G:693660018;T:723579965;N:59869,49,49,,,717580081,706848901,693660018,723579965,59869,SRX175054,SRS353007,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.97017,0.97095,0.09011,0.0904,0.71439,0.7151,0.49752,0.49683,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36497,SRR535926,SRX175043,SRS353006,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data vanglWT was created from 37 pooled wildtype fish that were the siblings vangl2m209 mutants vanglMUT.,Miller vanglWT.bam,Miller vanglWT.bam,,,,,,,,,,,Miller vanglWT.bam,Miller vanglWT.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,VanglWT.bam,bam,2487003183.0,26607574.0,Miller vanglWT.bam,0:49 1:49,A:625766450;C:621286922;G:609501341;T:630396047;N:52423,49,49,,,625766450,621286922,609501341,630396047,52423,SRX175043,SRS353006,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.97041,0.97032,0.08936,0.08869,0.71735,0.71681,0.48969,0.48984,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36498,SRR535913,SRX175029,SRS353004,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data kroxMUT was created from 30 pooled egr2bfh227 fish that were the siblings kroxWT.,Miller kroxMUT.bam,Miller kroxMUT.bam,,,,,,,,,,,Miller kroxMUT.bam,Miller kroxMUT.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,Krox20MUT.bam,bam,1779155847.0,19063863.0,Miller kroxMUT.bam,0:49 1:49,A:448798777;C:443091006;G:434890915;T:452337046;N:38103,49,49,,,448798777,443091006,434890915,452337046,38103,SRX175029,SRS353004,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.96852,0.96931,0.08951,0.08916,0.71334,0.71419,0.49323,0.48676,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36499,SRR535890,SRX175007,SRS353003,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data kroxWT was created from 30 pooled wildtype fish that were the siblings of egr2bfh227 mutants kroxMUT.,Miller kroxWT.bam,Miller kroxWT.bam,,,,,,,,,,,Miller kroxWT.bam,Miller kroxWT.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,Krox20WT.bam,bam,1682682099.0,18042374.0,Miller kroxWT.bam,0:49 1:49,A:424802426;C:418598739;G:411023668;T:428221805;N:35461,49,49,,,424802426,418598739,411023668,428221805,35461,SRX175007,SRS353003,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.96899,0.96898,0.09334,0.09311,0.71175,0.7134,0.49346,0.49545,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36500,SRR535852,SRX174969,SRS353001,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data hox80 was created from 80 pooled hoxb1bb1219 fish that were the siblings of wt80.,Miller hox80.bam,Miller hox80.bam,,,,,,,,,,,Miller hox80.bam,Miller hox80.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,hox80.bam,bam,1678151069.0,18115874.0,Miller hox80.bam,0:49 1:49,A:431345472;C:411044967;G:399581415;T:436154722;N:24493,49,49,,,431345472,411044967,399581415,436154722,24493,SRX174969,SRS353001,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.9641,0.96398,0.06923,0.06967,0.67292,0.67351,0.47172,0.46487,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36501,SRR535851,SRX174968,SRS352997,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data wt80 was created from 80 pooled wildtype fish that were the siblings of hoxb1bb1219 mutants hox80.,Miller wt80.bam,Miller wt80.bam,,,,,,,,,,,Miller wt80.bam,Miller wt80.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,wt80.bam,bam,1549792776.0,16755260.0,Miller wt80.bam,0:49 1:49,A:398834131;C:378881149;G:368968613;T:403086206;N:22677,49,49,,,398834131,378881149,368968613,403086206,22677,SRX174968,SRS352997,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.96256,0.96363,0.07093,0.07144,0.67008,0.67073,0.46471,0.46452,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36502,SRR535850,SRX174967,SRS353000,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data hox40 was created from 40 pooled hoxb1bb1219 fish that were the siblings of wt40.,Miller hox40.bam,Miller hox40.bam,,,,,,,,,,,Miller hox40.bam,Miller hox40.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,hox40.bam,bam,1587319671.0,17144843.0,Miller hox40.bam,0:49 1:49,A:408875513;C:388394610;G:376914302;T:413112173;N:23073,49,49,,,408875513,388394610,376914302,413112173,23073,SRX174967,SRS353000,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.9632,0.96359,0.07035,0.07053,0.67194,0.67304,0.46695,0.46523,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36503,SRR535849,SRX174966,SRS352996,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data wt40 was created from 40 pooled wildtype fish that were the siblings of hoxb1bb1219 mutants hox40.,Miller wt40.bam,Miller wt40.bam,,,,,,,,,,,Miller wt40.bam,Miller wt40.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,,wt40.bam,bam,1824107271.0,19685973.0,Miller wt40.bam,0:49 1:49,A:469488475;C:446295210;G:434332337;T:473964800;N:26449,49,49,,,469488475,446295210,434332337,473964800,26449,SRX174966,SRS352996,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.96306,0.96378,0.07263,0.07309,0.66888,0.6686,0.46488,0.46371,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36504,SRR535848,SRX174964,SRS352998,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data hox20 was created from 20 pooled hoxb1bb1219 fish that were the siblings of wt20.,Miller hox20.bam,Miller hox20.bam,,,,,,,,,,,Miller hox20.bam,Miller hox20.bam,1,50 bp Paired End,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</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>,SRP014772,,,hox20.bam,bam,2051648571.0,22151528.0,Miller hox20.bam,0:49 1:49,A:528770281;C:501621137;G:487051170;T:534176088;N:29895,49,49,,,528770281,501621137,487051170,534176088,29895,SRX174964,SRS352998,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.9629,0.96282,0.07314,0.07288,0.6714,0.67125,0.4665,0.4637,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36505,SRR535847,SRX174962,SRS352960,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data wt20 was created from 20 pooled wildtype fish that were the siblings of hoxb1bb1219 mutants hox20.,Miller wt20.bam,Miller wt20.bam,,,,,,,,,,,Miller wt20.bam,Miller wt20.bam,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<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>,SRP014772,,remap:MT:NC 002333.2,,,2122753696.0,22943089.0,Miller wt20.bam,0:49 1:49,A:545005462;C:520636497;G:506035162;T:551045523;N:31052,49,49,,,545005462,520636497,506035162,551045523,31052,SRX174962,SRS352960,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.96321,0.96343,0.08236,0.08218,0.67038,0.67075,0.46956,0.47045,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
41593,SRR392106,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009841,,,c1-2_1.fq c1-2_2.fq,fastq fastq,855494000.0,4502600.0,Control Sampe 1,0:100 1:90,A:217839807;C:202017646;G:207454208;T:227797566;N:384773,100,90,,,217839807,202017646,207454208,227797566,384773,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.87575,0.93454,0.06936,0.08546,0.82513,0.82306,0.49603,0.49334,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41594,SRR392108,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009841,,,c2-2_1.fq c2-2_2.fq,fastq fastq,1238874100.0,6520390.0,Control Sampe 2,0:100 1:90,A:316162781;C:292160612;G:299402161;T:330578118;N:570428,100,90,,,316162781,292160612,299402161,330578118,570428,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.89891,0.94864,0.03863,0.04738,0.8673,0.86531,0.28488,0.27076,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41595,SRR392109,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009841,,,c3-2_2.fq c3-2_1.fq,fastq fastq,2412101476.0,12830327.0,Control Sampe 3,0:100 1:88,A:611075174;C:569003408;G:589175071;T:641747898;N:1099925,100,88,,,611075174,569003408,589175071,641747898,1099925,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.87563,0.94341,0.03506,0.0441,0.83063,0.82795,0.41995,0.41226,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41596,SRR392110,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009841,,,v1_2.fq v1_1.fq,fastq fastq,1549099640.0,8153156.0,Case sampe 1,0:100 1:90,A:412607118;C:353282622;G:359371048;T:423373718;N:465134,100,90,,,412607118,353282622,359371048,423373718,465134,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.92368,0.9462,0.0604,0.06838,0.81249,0.81578,0.47008,0.4761,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41597,SRR392111,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009841,,,v2_1.fq v2_2.fq,fastq fastq,1465445712.0,7794924.0,Case sampe 2,0:100 1:88,A:387149663;C:337675800;G:340143929;T:400109622;N:366698,100,88,,,387149663,337675800,340143929,400109622,366698,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.92047,0.94711,0.05494,0.06325,0.81255,0.8143,0.48839,0.47383,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41598,SRR402758,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP009841,,,v3_2.fq v3_1.fq,fastq fastq,1025249164.0,5453453.0,Case sampe 3,0:100 1:88,A:261599009;C:242254683;G:249423008;T:271717829;N:254635,100,88,,,261599009,242254683,249423008,271717829,254635,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.93668,0.95934,0.02982,0.03449,0.81347,0.8196,0.47392,0.47176,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System