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
33369,SRR30159204,SRX25626516,SRS22271512,SRP524652,PRJNA1145276,The RNA sequence analysis post lossing tango6,PRJNA1145276,Other,To detect RNA expression level difference post lost of TANGO6,,,,,Mutant 2,,strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.8 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal,,,,,,,,,Mutant 2,Li lab 003 4,Li lab 003 4,RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 6 g of total RNA was used for construction of sequencing libraries.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP524652,,,7c166f592635e7a5f904d56dd661e1cc mut-2_1.fq.gz.gz 3adc1733ac4cb77beca49461cb17544b mut-2_2.fq.gz.gz,fastq fastq,5518961400.0,18396538.0,3adc1733ac4cb77beca49461cb17544b mut 2 2.fq.gz.gz,0:150 1:150,A:1469924277;C:1285547670;G:1307420673;T:1455990444;N:78336,150,150,,,1469924277,1285547670,1307420673,1455990444,78336,SRX25626516,SRS22271512,SRA1941919,"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing","Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences",2,0.96085,0.95919,0.05548,0.05519,0.7207,0.72178,0.47759,0.47549,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-08-07,Larval,Larval,Undetermined,Undetermined
33370,SRR30159205,SRX25626515,SRS22271511,SRP524652,PRJNA1145276,The RNA sequence analysis post lossing tango6,PRJNA1145276,Other,To detect RNA expression level difference post lost of TANGO6,,,,,Mutant 1,,strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.7 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal,,,,,,,,,Mutant 1,Li lab 003 3,Li lab 003 3,RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 5 g of total RNA was used for construction of sequencing libraries.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP524652,,,39cb7947119cec5afac3df66c0ae0048 mut-1_1.fq.gz.gz 1bfc59902758bb1cbf8eb4549d3375fd mut-1_2.fq.gz.gz,fastq fastq,5947120500.0,19823735.0,1bfc59902758bb1cbf8eb4549d3375fd mut 1 2.fq.gz.gz,0:150 1:150,A:1567673549;C:1401761128;G:1423907629;T:1553701047;N:77147,150,150,,,1567673549,1401761128,1423907629,1553701047,77147,SRX25626515,SRS22271511,SRA1941919,"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing","Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences",2,0.96303,0.96203,0.05003,0.04984,0.72271,0.72299,0.47608,0.47831,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-08-07,Larval,Larval,Undetermined,Undetermined
33371,SRR30159206,SRX25626514,SRS22271510,SRP524652,PRJNA1145276,The RNA sequence analysis post lossing tango6,PRJNA1145276,Other,To detect RNA expression level difference post lost of TANGO6,,,,,Wild type 2,,strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.6 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal,,,,,,,,,Wild type 2,Li lab 003 2,Li lab 003 2,RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 4 g of total RNA was used for construction of sequencing libraries.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP524652,,,4376e7007befe0cf23ffa7f9dd62512c sib-3_1.fq.gz.gz da4d46fd26ca22e90409489640659b1c sib-3_2.fq.gz.gz,fastq fastq,6113935200.0,20379784.0,4376e7007befe0cf23ffa7f9dd62512c sib 3 1.fq.gz.gz,0:150 1:150,A:1609711214;C:1443384557;G:1461871812;T:1598876167;N:91450,150,150,,,1609711214,1443384557,1461871812,1598876167,91450,SRX25626514,SRS22271510,SRA1941919,"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing","Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences",2,0.95947,0.9591,0.04902,0.0492,0.71707,0.71796,0.46871,0.4604,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-08-07,Larval,Larval,Undetermined,Undetermined
33372,SRR30159207,SRX25626513,SRS22271509,SRP524652,PRJNA1145276,The RNA sequence analysis post lossing tango6,PRJNA1145276,Other,To detect RNA expression level difference post lost of TANGO6,,,,,Wild type 1,,strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.5 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal,,,,,,,,,Wild type 1,Li lab 003 1,Li lab 003 1,RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 3 g of total RNA was used for construction of sequencing libraries.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP524652,,,319b2e8b61305a8937eb903a7a20a2e7 sib-2_1.fq.gz.gz 4a84982431b5360126f279ceabf00548 sib-2_2.fq.gz.gz,fastq fastq,6351813000.0,21172710.0,319b2e8b61305a8937eb903a7a20a2e7 sib 2 1.fq.gz.gz,0:150 1:150,A:1674596701;C:1497102731;G:1525030471;T:1654985592;N:97505,150,150,,,1674596701,1497102731,1525030471,1654985592,97505,SRX25626513,SRS22271509,SRA1941919,"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing","Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences",2,0.96469,0.96334,0.04679,0.04633,0.73119,0.73198,0.47359,0.47265,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-08-07,Larval,Larval,Undetermined,Undetermined
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
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
36600,SRR633516,SRX209919,SRS379598,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae maintained at control conditiion  replicate 1,ck1,,,,,,,,,,,dataset of ck1,Seq1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,ck1_run2_R1.fastq.gz ck1_run2_R2.fastq.gz,fastq fastq,1425533040.0,19799070.0,Run 1,0:36 1:36,A:346892627;C:359716472;G:360029628;T:357662709;N:1231604,36,36,,,346892627,359716472,360029628,357662709,1231604,SRX209919,SRS379598,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93467,0.92945,0.06912,0.06892,0.67101,0.67233,0.45594,0.45635,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-16,Larval,Larval,Undetermined,Undetermined
36601,SRR633554,SRX210639,SRS379606,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to hypoxia stress  replicate 3,hypo3,,,,,,,,,,,dataset for sample hypo3,Seq9,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,1048140792.0,14557511.0,hypo3 run1,0:36 1:36,A:259618733;C:259785246;G:262230196;T:266244448;N:262169,36,36,,,259618733,259785246,262230196,266244448,262169,SRX210639,SRS379606,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93986,0.93562,0.06965,0.06854,0.67006,0.67131,0.43686,0.45545,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-18,Larval,Larval,Undetermined,Undetermined
36602,SRR633555,SRX210639,SRS379606,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to hypoxia stress  replicate 3,hypo3,,,,,,,,,,,dataset for sample hypo3,Seq9,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,hypo3_run2_R2.fastq.gz,fastq,1000001376.0,13888908.0,hypo3 run2,0:36 1:36,A:246155193;C:248766521;G:251127505;T:252483880;N:1468277,36,36,,,246155193,248766521,251127505,252483880,1468277,SRX210639,SRS379606,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93954,0.93167,0.06689,0.06675,0.67322,0.6748,0.46287,0.4641,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2013-12-13,Larval,Larval,Undetermined,Undetermined
36603,SRR633552,SRX210638,SRS379605,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to hypoxia stress  replicate 2,hypo2,,,,,,,,,,,dataset for sample hypo2,Seq8,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,944842752.0,13122816.0,hypo2 run1,0:36 1:36,A:230936699;C:236712021;G:238060792;T:238878037;N:255203,36,36,,,230936699,236712021,238060792,238878037,255203,SRX210638,SRS379605,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93909,0.93309,0.07087,0.07105,0.6672,0.66813,0.46107,0.45873,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-18,Larval,Larval,Undetermined,Undetermined
36604,SRR633553,SRX210638,SRS379605,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to hypoxia stress  replicate 2,hypo2,,,,,,,,,,,dataset for sample hypo2,Seq8,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,hypo2_run2_R2.fastq.gz,fastq,988361568.0,13727244.0,hypo2 run2,0:36 1:36,A:240212534;C:248205313;G:250004116;T:248599375;N:1340230,36,36,,,240212534,248205313,250004116,248599375,1340230,SRX210638,SRS379605,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.94029,0.93226,0.07174,0.0704,0.67129,0.67142,0.44913,0.45448,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2013-12-13,Larval,Larval,Undetermined,Undetermined
36605,SRR633550,SRX210637,SRS379604,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to hypoxia stress  replicate 1,hypo1,,,,,,,,,,,dataset for sample hypo1,Seq7,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,1111534488.0,15437979.0,hypo1 run1,0:36 1:36,A:273016370;C:277718934;G:279150260;T:281380668;N:268256,36,36,,,273016370,277718934,279150260,281380668,268256,SRX210637,SRS379604,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93448,0.92737,0.07734,0.077,0.66886,0.67012,0.45226,0.45356,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-17,Larval,Larval,Undetermined,Undetermined
36606,SRR633551,SRX210637,SRS379604,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to hypoxia stress  replicate 1,hypo1,,,,,,,,,,,dataset for sample hypo1,Seq7,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,hypo1_run2_R2.fastq.gz,fastq,1086628536.0,15092063.0,hypo run2,0:36 1:36,A:265451380;C:271989493;G:274094744;T:273520855;N:1572064,36,36,,,265451380,271989493,274094744,273520855,1572064,SRX210637,SRS379604,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.9313,0.92722,0.07613,0.07533,0.67511,0.67468,0.45532,0.4554,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-17,Larval,Larval,Undetermined,Undetermined
36607,SRR633548,SRX210636,SRS379603,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to cold stress  replicate 3,cold3,,,,,,,,,,,dataset for sample cold3,Seq6,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,cold3_run1_R2.fastq.gz,fastq,856370016.0,11894028.0,cold3 run1,0:36 1:36,A:203894018;C:218965032;G:223278100;T:210022674;N:210192,36,36,,,203894018,218965032,223278100,210022674,210192,SRX210636,SRS379603,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.9356,0.93083,0.06354,0.06342,0.67495,0.67659,0.46514,0.46632,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2013-12-13,Larval,Larval,Undetermined,Undetermined
36608,SRR633549,SRX210636,SRS379603,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to cold stress  replicate 3,cold3,,,,,,,,,,,dataset for sample cold3,Seq6,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,912477384.0,12673297.0,cold3 run2,0:36 1:36,A:216126045;C:233918163;G:238615002;T:222532152;N:1286022,36,36,,,216126045,233918163,238615002,222532152,1286022,SRX210636,SRS379603,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93707,0.93034,0.06328,0.06231,0.68199,0.68154,0.45852,0.45712,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-17,Larval,Larval,Undetermined,Undetermined
36609,SRR633546,SRX210635,SRS379602,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to cold stress  replicate 2,cold2,,,,,,,,,,,dataset for sample cold2,Seq5,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,cold2_run1_R2.fastq.gz,fastq,758704104.0,10537557.0,cold2 run1,0:36 1:36,A:183694352;C:191591559;G:194571241;T:188644215;N:202737,36,36,,,183694352,191591559,194571241,188644215,202737,SRX210635,SRS379602,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.9355,0.93037,0.07579,0.07546,0.67758,0.67799,0.46336,0.4537,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-17,Larval,Larval,Undetermined,Undetermined
36610,SRR633547,SRX210635,SRS379602,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to cold stress  replicate 2,cold2,,,,,,,,,,,dataset for sample cold2,Seq5,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,758269944.0,10531527.0,cold2 run2,0:36 1:36,A:182477606;C:192044319;G:195270817;T:187486180;N:991022,36,36,,,182477606,192044319,195270817,187486180,991022,SRX210635,SRS379602,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93526,0.92936,0.07437,0.07319,0.68252,0.68243,0.45977,0.45219,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-17,Larval,Larval,Undetermined,Undetermined
36611,SRR633544,SRX210634,SRS379601,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to cold stress  replicate 1,cold1,,,,,,,,,,,dataset for sample cold1,Seq4,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,939174120.0,13044085.0,cold1 run1,0:36 1:36,A:229908173;C:234619234;G:239161528;T:235262399;N:222786,36,36,,,229908173,234619234,239161528,235262399,222786,SRX210634,SRS379601,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.92711,0.91958,0.08119,0.08052,0.67032,0.67249,0.4669,0.4661,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-17,Larval,Larval,Undetermined,Undetermined
36612,SRR633545,SRX210634,SRS379601,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae exposed to cold stress  replicate 1,cold1,,,,,,,,,,,dataset for sample cold1,Seq4,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,cold1_run2_R2.fastq.gz,fastq,969327360.0,13462880.0,cold1 run2,0:36 1:36,A:236017916;C:242777395;G:247690199;T:241486770;N:1355080,36,36,,,236017916,242777395,247690199,241486770,1355080,SRX210634,SRS379601,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.92225,0.91649,0.08088,0.07942,0.67811,0.67819,0.47395,0.47096,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2013-12-13,Larval,Larval,Undetermined,Undetermined
36613,SRR633542,SRX210633,SRS379600,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae maintained at control condition  replicate 3,ck3,,,,,,,,,,,dataset for sample ck3,Seq3,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,712122912.0,9890596.0,ck3 run1,0:36 1:36,A:173202209;C:178330394;G:181430842;T:178980355;N:179112,36,36,,,173202209,178330394,181430842,178980355,179112,SRX210633,SRS379600,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93432,0.92622,0.07444,0.07347,0.66267,0.66381,0.45819,0.45458,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-17,Larval,Larval,Undetermined,Undetermined
36614,SRR633543,SRX210633,SRS379600,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae maintained at control condition  replicate 3,ck3,,,,,,,,,,,dataset for sample ck3,Seq3,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,690216696.0,9586343.0,ck3 run2,0:36 1:36,A:166782468;C:173577192;G:176360566;T:172494787;N:1001683,36,36,,,166782468,173577192,176360566,172494787,1001683,SRX210633,SRS379600,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93384,0.92481,0.07221,0.07087,0.66813,0.6692,0.45481,0.4573,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-16,Larval,Larval,Undetermined,Undetermined
36615,SRR633540,SRX210632,SRS379599,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae maintained at control condition  replicate 2,ck2,,,,,,,,,,,dataset for sample ck2,Seq2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,ck2_run1_R1.fastq.gz ck2_run1_R2.fastq.gz,fastq fastq,893329776.0,12407358.0,run1,0:36 1:36,A:218731725;C:223935822;G:225438843;T:224982678;N:240708,36,36,,,218731725,223935822,225438843,224982678,240708,SRX210632,SRS379599,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.92555,0.92021,0.07993,0.08001,0.6631,0.66358,0.46925,0.46964,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2013-12-13,Larval,Larval,Undetermined,Undetermined
36616,SRR633541,SRX210632,SRS379599,SRP017563,PRJNA183864,Zebrafish larvae exposed to cold or hypoxia stress,PRJNA183864,Other,To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses  larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h  and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure  RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.,,,1,zebrafish larvae maintained at control condition  replicate 2,ck2,,,,,,,,,,,dataset for sample ck2,Seq2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP017563,,,,,886248648.0,12309009.0,run2,0:36 1:36,A:215735507;C:222732158;G:224616280;T:221967000;N:1197703,36,36,,,215735507,222732158,224616280,221967000,1197703,SRX210632,SRS379599,SRA062881,"Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.92626,0.91948,0.07987,0.07869,0.66785,0.66778,0.46701,0.4675,36,36,B,B,biological fallback assumption,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,China,2012-12-16,Larval,Larval,Undetermined,Undetermined
72097,SRR22207161,SRX18185147,SRS15683480,SRP406513,PRJNA898663,zebrafish Raw sequence reads,PRJNA898663,Other,High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish,,,,,L3,,isolate:Loxhd1b 3|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RNA: loxhd1b morpholino 3,GCS6,GCS6,Next generation sequencing library preparations were constructed according to the manufacturers protocol.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP406513,,,L3_combined_R1.fastq.gz L3_combined_R2.fastq.gz,fastq fastq,6143010000.0,20476700.0,L3 combined R1.fastq.gz,0:150 1:150,A:1595745772;C:1478410203;G:1489224712;T:1579586384;N:42929,150,150,,,1595745772,1478410203,1489224712,1579586384,42929,SRX18185147,SRS15683480,SRA1535247,Shandong Provincial Hospital|Department of Clinical Laboratory,Shandong Provincial Hospital,2,0.95627,0.95623,0.04743,0.04704,0.70256,0.7068,0.47182,0.4714,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2022-11-06,Larval,Larval,Undetermined,Undetermined
72098,SRR22207162,SRX18185146,SRS15683479,SRP406513,PRJNA898663,zebrafish Raw sequence reads,PRJNA898663,Other,High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish,,,,,L2,,isolate:Loxhd1b 2|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RNA: loxhd1b morpholino 2,GCS5,GCS5,Next generation sequencing library preparations were constructed according to the manufacturers protocol.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP406513,,,L2_combined_R1.fastq.gz L2_combined_R2.fastq.gz,fastq fastq,6424738200.0,21415794.0,L2 combined R1.fastq.gz,0:150 1:150,A:1671624607;C:1543603819;G:1552613091;T:1656850928;N:45755,150,150,,,1671624607,1543603819,1552613091,1656850928,45755,SRX18185146,SRS15683479,SRA1535247,Shandong Provincial Hospital|Department of Clinical Laboratory,Shandong Provincial Hospital,2,0.95661,0.95668,0.04747,0.04742,0.68856,0.69179,0.47314,0.48109,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2022-11-06,Larval,Larval,Undetermined,Undetermined
72099,SRR22207163,SRX18185145,SRS15683478,SRP406513,PRJNA898663,zebrafish Raw sequence reads,PRJNA898663,Other,High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish,,,,,L1,,isolate:Loxhd1b 1|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RNA: loxhd1b morpholino 1,GCS4,GCS4,Next generation sequencing library preparations were constructed according to the manufacturers protocol.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP406513,,,L1_combined_R1.fastq.gz L1_combined_R2.fastq.gz,fastq fastq,7191693900.0,23972313.0,L1 combined R1.fastq.gz,0:150 1:150,A:1864938414;C:1733274971;G:1741654024;T:1851774229;N:52262,150,150,,,1864938414,1733274971,1741654024,1851774229,52262,SRX18185145,SRS15683478,SRA1535247,Shandong Provincial Hospital|Department of Clinical Laboratory,Shandong Provincial Hospital,2,0.95471,0.95533,0.05078,0.05161,0.67844,0.68191,0.47707,0.48159,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2022-11-06,Larval,Larval,Undetermined,Undetermined
72100,SRR22207164,SRX18185144,SRS15683477,SRP406513,PRJNA898663,zebrafish Raw sequence reads,PRJNA898663,Other,High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish,,,,,C3,,isolate:control 3|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RNA: control 3,GCS3,GCS3,Next generation sequencing library preparations were constructed according to the manufacturers protocol.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP406513,,,C3_combined_R1.fastq.gz C3_combined_R2.fastq.gz,fastq fastq,6332394900.0,21107983.0,C3 combined R1.fastq.gz,0:150 1:150,A:1627554436;C:1541108160;G:1544576517;T:1619111254;N:44533,150,150,,,1627554436,1541108160,1544576517,1619111254,44533,SRX18185144,SRS15683477,SRA1535247,Shandong Provincial Hospital|Department of Clinical Laboratory,Shandong Provincial Hospital,2,0.95993,0.95944,0.04103,0.04133,0.68296,0.68779,0.48812,0.47385,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2022-11-06,Larval,Larval,Undetermined,Undetermined
72101,SRR22207165,SRX18185143,SRS15683476,SRP406513,PRJNA898663,zebrafish Raw sequence reads,PRJNA898663,Other,High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish,,,,,C2,,isolate:control 2|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RNA: control 2,GCS2,GCS2,Next generation sequencing library preparations were constructed according to the manufacturers protocol.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP406513,,,C2_combined_R1.fastq.gz C2_combined_R2.fastq.gz,fastq fastq,6442334100.0,21474447.0,C2 combined R1.fastq.gz,0:150 1:150,A:1656988931;C:1570298030;G:1573573169;T:1641411583;N:62387,150,150,,,1656988931,1570298030,1573573169,1641411583,62387,SRX18185143,SRS15683476,SRA1535247,Shandong Provincial Hospital|Department of Clinical Laboratory,Shandong Provincial Hospital,2,0.95971,0.96117,0.03893,0.03968,0.70692,0.71169,0.47551,0.47899,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2022-11-06,Larval,Larval,Undetermined,Undetermined
72102,SRR22207166,SRX18185142,SRS15683475,SRP406513,PRJNA898663,zebrafish Raw sequence reads,PRJNA898663,Other,High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish,,,,,C1,,isolate:control 1|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RNA: control 1,GCS1,GCS1,Next generation sequencing library preparations were constructed according to the manufacturers protocol.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP406513,,,C1_combined_R1.fastq.gz C1_combined_R2.fastq.gz,fastq fastq,6508720200.0,21695734.0,C1 combined R1.fastq.gz,0:150 1:150,A:1679478806;C:1581181952;G:1586326453;T:1661672060;N:60929,150,150,,,1679478806,1581181952,1586326453,1661672060,60929,SRX18185142,SRS15683475,SRA1535247,Shandong Provincial Hospital|Department of Clinical Laboratory,Shandong Provincial Hospital,2,0.9598,0.96029,0.04091,0.04106,0.70834,0.71171,0.4832,0.48953,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2022-11-06,Larval,Larval,Undetermined,Undetermined