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
29215,SRR27489731,SRX23160978,SRS20111136,SRP483112,PRJNA1056276,five prime UTR MPRA during early zebrafish embryogenesis,PRJNA1056276,Other,The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.,,,RNA product,control RNA library,RNA mMessage MPRA library,,strain:not applicable|age:not applicable|dev stage:not applicable|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:not applicable|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:not applicable|growth protocol:not applicable|sample type:IVT mRNA|sample number:50|replicate:unique sample|BioSampleModel:Model organism or animal,,,,,,,,,control RNA library,Library 50,Library 50,PCR product was amplified from DNA plasmid pool with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.,,,OTHER,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483112,,,BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R2_001_MM_1.fastq.gz,fastq fastq,16695252486.0,55282293.0,BSSE QGF 206685 HGWLYDSX3 3 RNA mMessage MPRA library test GGTTATAA GATATCGA S50 L003 R1 001 MM 1.fastq.gz,0:151 1:151,A:4275447149;C:4413405571;G:3936523108;T:4069049357;N:827301,151,151,,,4275447149,4413405571,3936523108,4069049357,827301,SRX23160978,SRS20111136,SRA1775336,University of Basel|Biozentrum Basel,University of Basel,2,0.02176,0.00021,0.00058,2e-05,0.99056,0.99933,0.41475,0.48571,151,151,T,T,mates < 9% mapping rate,illumina,novaseq_era,5prime,other,unknown,bulk,unknown,unknown,,Switzerland,2024-01-11,Undetermined,Embryo,Undetermined,Embryo Imprecise
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
36665,SRR800045,SRX257154,SRS405708,SRP020008,PRJNA193544,Danio rerio strain:Tubingen Epigenomics,PRJNA193544,Other,Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.,,pubmed:23663776,Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,Generic sample from Danio rerio,muscle RNAseq totalRNARibominus,,strain:Tubingen|label:PE: paired end  SE: single end|development stage:muscle,,,,,,,,,muscle RNAseq totalRNARibominus,muscle RNAseq totalRNARibominus,9084X1,Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 1000,<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>,SRP020008,,,muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz,Illumina native,3506573750.0,70131475.0,9084X1 120420 SN141 0500 AD0TG5ACXX 5,0:50,A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806,50,,,,872717534,808774955,1036781008,777391447,10908806,SRX257154,SRS405708,SRA072148,University of Utah|Brad Cairns Lab,University of Utah,1,0.61428,,0.09813,,0.89305,,0.6908,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,United States,2013-05-07,Undetermined,Embryo,Muscle,Muscular System
36668,SRR800037,SRX257149,SRS405106,SRP020008,PRJNA193544,Danio rerio strain:Tubingen Epigenomics,PRJNA193544,Other,Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.,,pubmed:23663776,Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,Generic sample from Danio rerio,egg RNAseq totalRNARibominus,,strain:Tubingen|label:PE: paired end  SE: single end|dev stage:egg,,,,,,,,,egg RNAseq totalRNARibominus,egg RNAseq totalRNARibominus,7784X1,Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,<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>,SRP020008,,,,,3584440000.0,71688800.0,7784X1 110323 SN141 0332 A81FDVABXX 8,0:50,A:1013532157;C:812179975;G:992916103;T:765761452;N:50313,50,,,,1013532157,812179975,992916103,765761452,50313,SRX257149,SRS405106,SRA072148,University of Utah|Brad Cairns Lab,University of Utah,1,0.87304,,0.12853,,0.81988,,0.80407,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,United States,2013-04-01,Undetermined,Embryo,Undetermined,Embryo Imprecise
36669,SRR800038,SRX257149,SRS405106,SRP020008,PRJNA193544,Danio rerio strain:Tubingen Epigenomics,PRJNA193544,Other,Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.,,pubmed:23663776,Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,Generic sample from Danio rerio,egg RNAseq totalRNARibominus,,strain:Tubingen|label:PE: paired end  SE: single end|dev stage:egg,,,,,,,,,egg RNAseq totalRNARibominus,egg RNAseq totalRNARibominus,7784X1,Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,<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>,SRP020008,,,,,2794240450.0,55884809.0,7784X1 110119 SN141 0323 B8162JABXX 8,0:50,A:792200981;C:632130044;G:772351331;T:596980885;N:577209,50,,,,792200981,632130044,772351331,596980885,577209,SRX257149,SRS405106,SRA072148,University of Utah|Brad Cairns Lab,University of Utah,1,0.86104,,0.12909,,0.82266,,0.80894,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,United States,2013-04-01,Undetermined,Embryo,Undetermined,Embryo Imprecise
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
42451,SRR5590336,SRX2847138,SRS2220119,SRP115073,PRJNA387549,zebrafish Raw sequence reads,PRJNA387549,Metagenomics,The study was to unravel the complex toxic effects of chemical contaminants on the health of organisms as based on different levels of biological profling.,,,,without xxx and with difenoconazole,CK D 50 D 500,,strain:AB|isolate:embryo|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:pooled male and female|tissue:whole individual|BioSampleModel:Model organism or animal,,,,,,,,,RNA Sequencing in zebrafish without xxx and with difenoconazole,zebrafish RNA Sequencing project,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>6</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>,SRP115073,,,CK_1_1.fq.gz CK_1_2.fq.gz CK_2_1.fq.gz CK_3_1.fq.gz CK_3_2.fq.gz D_500_1_1.fq.gz D_500_1_2.fq.gz D_500_2_1.fq.gz D_500_2_2.fq.gz D_500_3_1.fq.gz D_500_3_2.fq.gz D_50_1_1.fq.gz D_50_1_2.fq.gz D_50_3_2.fq.gz D_50_3_1.fq.gz D_50_2_2.fq.gz D_50_2_1.fq.gz CK_2_2.fq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,81797448900.0,272658163.0,zebrafish RNA Seq,0:150 1:150,A:21743331485;C:19042575463;G:19378823851;T:21630253992;N:2464109,150,150,,,21743331485,19042575463,19378823851,21630253992,2464109,SRX2847138,SRS2220119,SRA564978,China Agricultural University|College of Science,China Agricultural University,2,0.91941,0.92018,0.10515,0.10533,0.67939,0.68552,0.46739,0.46494,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-04-14,Undetermined,Embryo,Whole Organism,All anatomical structures
62799,SRR13381327,SRX9804263,SRS7988468,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,c 1,,sample title for replicate:c 1|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,c 1,c 1,c 1,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,c1-R1.fq.gz.gz c1-R2.fq.gz.gz,fastq fastq,3188746630.0,21313115.0,c1 R1.fq.gz.gz,0:149.61,A:907108265;C:694245090;G:701033373;T:886334111;N:25791,149,,,,907108265,694245090,701033373,886334111,25791,SRX9804263,SRS7988468,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.88484,,0.19252,,0.72153,,0.51441,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62800,SRR13381328,SRX9804262,SRS7988467,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,b 3,,sample title for replicate:b 3|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,b 3,b 3,b 3,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,b3-R1.fq.gz.gz b3-R2.fq.gz.gz,fastq fastq,3410851764.0,22784502.0,b3 R1.fq.gz.gz,0:149.70,A:978915230;C:735962678;G:739687608;T:956258485;N:27763,149,,,,978915230,735962678,739687608,956258485,27763,SRX9804262,SRS7988467,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.90179,,0.18495,,0.71541,,0.52314,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62801,SRR13381329,SRX9804261,SRS7988466,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,b 2,,sample title for replicate:b 2|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,b 2,b 2,b 2,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,b2-R1.fq.gz.gz b2-R2.fq.gz.gz,fastq fastq,3152478044.0,21115710.0,b2 R1.fq.gz.gz,0:149.30,A:947002080;C:630086332;G:638703847;T:936677512;N:8273,149,,,,947002080,630086332,638703847,936677512,8273,SRX9804261,SRS7988466,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.80951,,0.24776,,0.77906,,0.57691,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62802,SRR13381330,SRX9804260,SRS7988465,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,b 1,,sample title for replicate:b 1|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,b 1,b 1,b 1,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,b1-R1.fq.gz.gz b1-R2.fq.gz.gz,fastq fastq,3352598587.0,22415585.0,b1 R1.fq.gz.gz,0:149.57,A:976446828;C:708370059;G:713539822;T:954214882;N:26996,149,,,,976446828,708370059,713539822,954214882,26996,SRX9804260,SRS7988465,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.90048,,0.22988,,0.71216,,0.4927,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62803,SRR13381331,SRX9804259,SRS7988464,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,a 3,,sample title for replicate:a 3|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,a 3,a 3,a 3,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,a3-R1.fq.gz.gz a3-R2.fq.gz.gz,fastq fastq,3171167510.0,21201111.0,a3 R1.fq.gz.gz,0:149.58,A:904575002;C:687927904;G:693921563;T:884717279;N:25762,149,,,,904575002,687927904,693921563,884717279,25762,SRX9804259,SRS7988464,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.87972,,0.19211,,0.73001,,0.51068,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62804,SRR13381332,SRX9804258,SRS7988463,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,a 2,,sample title for replicate:a 2|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,a 2,a 2,a 2,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,a2-R1.fq.gz.gz a2-R2.fq.gz.gz,fastq fastq,2970077328.0,19894385.0,a2 R1.fq.gz.gz,0:149.29,A:877143980;C:609672974;G:615339733;T:867912969;N:7672,149,,,,877143980,609672974,615339733,867912969,7672,SRX9804258,SRS7988463,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.83922,,0.22546,,0.78386,,0.66266,,128,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62805,SRR13381333,SRX9804257,SRS7988462,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,a 1,,sample title for replicate:a 1|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,a 1,a 1,a 1,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,a1-R1.fq.gz.gz a1-R2.fq.gz.gz,fastq fastq,3355906399.0,22420666.0,a1 R1.fq.gz.gz,0:149.68,A:967471134;C:715589495;G:719383048;T:953453855;N:8867,149,,,,967471134,715589495,719383048,953453855,8867,SRX9804257,SRS7988462,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.88569,,0.2199,,0.71486,,0.4934,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62806,SRR13381334,SRX9804256,SRS7988461,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,0 3,,sample title for replicate:0 3|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,0 3,0 3,0 3,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,ck3-R1.fq.gz.gz ck3-R2.fq.gz.gz,fastq fastq,3338640528.0,22323417.0,ck3 R1.fq.gz.gz,0:149.56,A:950056740;C:724127980;G:729397822;T:935049323;N:8663,149,,,,950056740,724127980,729397822,935049323,8663,SRX9804256,SRS7988461,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.8797,,0.17422,,0.72092,,0.50968,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62807,SRR13381335,SRX9804255,SRS7988460,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,c 3,,sample title for replicate:c 3|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,c 3,c 3,c 3,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,c3-R1.fq.gz.gz c3-R2.fq.gz.gz,fastq fastq,3306682837.0,22088500.0,c3 R1.fq.gz.gz,0:149.70,A:931414367;C:728984036;G:734931077;T:911326441;N:26916,149,,,,931414367,728984036,734931077,911326441,26916,SRX9804255,SRS7988460,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.88469,,0.16886,,0.72308,,0.50922,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62808,SRR13381336,SRX9804254,SRS7988459,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,c 2,,sample title for replicate:c 2|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,c 2,c 2,c 2,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,c2-R1.fq.gz.gz c2-R2.fq.gz.gz,fastq fastq,3445029375.0,23065463.0,c2 R1.fq.gz.gz,0:149.36,A:1033514432;C:696726296;G:699357939;T:1015389477;N:41231,149,,,,1033514432,696726296,699357939,1015389477,41231,SRX9804254,SRS7988459,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.87331,,0.30599,,0.72671,,0.54303,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62809,SRR13381337,SRX9804253,SRS7988458,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,0 2,,sample title for replicate:0 2|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,0 2,0 2,0 2,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,ck2-R1.fq.gz ck2-R2.fq.gz,fastq fastq,3311324763.0,22134043.0,ck2 R1.fq.gz,0:149.60,A:979349608;C:681079542;G:688681630;T:962205302;N:8681,149,,,,979349608,681079542,688681630,962205302,8681,SRX9804253,SRS7988458,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.87651,,0.27982,,0.71821,,0.51125,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62810,SRR13381338,SRX9804252,SRS7988457,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,0 1,,sample title for replicate:0 1|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,0 1,0 1,0 1,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,ck1-R1.fq.gz ck1-R2.fq.gz,fastq fastq,3233079806.0,21640984.0,ck1 R1.fq.gz,0:149.40,A:929185111;C:690348531;G:699157160;T:914380522;N:8482,149,,,,929185111,690348531,699157160,914380522,8482,SRX9804252,SRS7988457,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.86295,,0.20583,,0.7208,,0.52194,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures