RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

44 rows where experiment.library_selection = "RT-PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Undetermined"

✎ View and edit SQL

This data as json, CSV (advanced)

devstage_curation_coarse 3

devstage_curation 3

tissue_curation_coarse 2

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation 1

  • Undetermined · 44 ✖

technology 1

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 44 ✖

experiment.library_selection 1

  • RT-PCR · 44 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
36666 36666 SRR800043 SRX257153 SRS405345 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 sphere RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq totalRNARibominus sphere RNAseq totalRNARibominus 7986X2 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     sphere_RNAseq_totalRNARibominus_SE_7986X2_110510_SN141_0338_AB06MWABXX_7.txt.gz Illumina native 3029181300.0 60583626.0 7986X2 110510 SN141 0338 AB06MWABXX 7 0:50 A:768949744;C:733340278;G:903149841;T:623482299;N:259138 50       768949744 733340278 903149841 623482299 259138 SRX257153 SRS405345 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.83515   0.15524   0.81209   0.81031   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2015-07-22 Blastula Embryo Undetermined Embryo Imprecise
36667 36667 SRR800044 SRX257153 SRS405345 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 sphere RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq totalRNARibominus sphere RNAseq totalRNARibominus 7986X2 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     sphere_RNAseq_totalRNARibominus_SE_7986X2_110606_SN141_0359_BD0D8KABXX_6.txt.gz Illumina native 3947123500.0 78942470.0 7986X2 110606 SN141 0359 BD0D8KABXX 6 0:50 A:1000468440;C:957437794;G:1171831772;T:817292633;N:92861 50       1000468440 957437794 1171831772 817292633 92861 SRX257153 SRS405345 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.81283   0.14906   0.81335   0.81698   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2015-07-22 Blastula Embryo Undetermined Embryo Imprecise
36668 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 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
72097 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 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 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 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 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 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

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;