{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"RT-PCR\", experiment.library_source = \"TRANSCRIPTOMIC\" and tissue_curation_coarse = \"Undetermined\"", "rows": [[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", null, null, null, null, "Mutant 2", null, "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", null, null, null, null, null, null, null, null, "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 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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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP524652", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller nhslMUT.bam", "Miller nhslMUT.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "fh131MUT.bam", "bam", 1826508618.0, 18449582.0, "Miller nhslMUT.bam", "0:99", "A:483532536;C:434813089;G:419760061;T:488362447;N:40485", 99, null, null, null, 483532536, 434813089, 419760061, 488362447, 40485, "SRX175096", "SRS353009", "SRA056859", "Fred Hutchinson Cancer Research Center|Moens", "Fred Hutchinson Cancer Research Center", 1, 0.98575, null, 0.08593, null, 0.71001, null, 0.48782, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller nhslWT.bam", "Miller nhslWT.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "fh131WT.bam", "bam", 3473158887.0, 35082413.0, "Miller nhslWT.bam", "0:99", "A:938335920;C:812249868;G:790639478;T:931852781;N:80840", 99, null, null, null, 938335920, 812249868, 790639478, 931852781, 80840, "SRX175077", "SRS353008", "SRA056859", "Fred Hutchinson Cancer Research Center|Moens", "Fred Hutchinson Cancer Research Center", 1, 0.98331, null, 0.07541, null, 0.71401, null, 0.47828, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller vanglMUT.bam", "Miller vanglMUT.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller vanglWT.bam", "Miller vanglWT.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller kroxMUT.bam", "Miller kroxMUT.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller kroxWT.bam", "Miller kroxWT.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller hox80.bam", "Miller hox80.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller wt80.bam", "Miller wt80.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller hox40.bam", "Miller hox40.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller wt40.bam", "Miller wt40.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, null, "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, null, null, 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", null, "United States", "2012-11-30", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [36504, "SRR535848", "SRX174964", "SRS352998", "SRP014772", "PRJNA172016", "Danio rerio strain:*AB Variation", "PRJNA172016", "Other", "Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life however identifying the causal mutations from such screens has long been the bottleneck in the process particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons alter transcript splicing or alter gene expression levels. Furthermore we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall we show that RNA Seq is a fast reliable and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller hox20.bam", "Miller hox20.bam", "1", "50 bp Paired End", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "1800Application ReadForward1", "SRP014772", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "Miller wt20.bam", "Miller wt20.bam", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "1000Application ReadForward11Application ReadReverse51", "SRP014772", null, "remap:MT:NC 002333.2", null, null, 2122753696.0, 22943089.0, "Miller wt20.bam", "0:49 1:49", "A:545005462;C:520636497;G:506035162;T:551045523;N:31052", 49, 49, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae maintained at control conditiion replicate 1", "ck1", null, null, null, null, null, null, null, null, null, null, "dataset of ck1", "Seq1", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, "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, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae exposed to hypoxia stress replicate 3", "hypo3", null, null, null, null, null, null, null, null, null, null, "dataset for sample hypo3", "Seq9", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, null, null, 1048140792.0, 14557511.0, "hypo3 run1", "0:36 1:36", "A:259618733;C:259785246;G:262230196;T:266244448;N:262169", 36, 36, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae exposed to hypoxia stress replicate 3", "hypo3", null, null, null, null, null, null, null, null, null, null, "dataset for sample hypo3", "Seq9", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, "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, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae exposed to hypoxia stress replicate 2", "hypo2", null, null, null, null, null, null, null, null, null, null, "dataset for sample hypo2", "Seq8", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, null, null, 944842752.0, 13122816.0, "hypo2 run1", "0:36 1:36", "A:230936699;C:236712021;G:238060792;T:238878037;N:255203", 36, 36, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae exposed to hypoxia stress replicate 2", "hypo2", null, null, null, null, null, null, null, null, null, null, "dataset for sample hypo2", "Seq8", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, "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, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae exposed to hypoxia stress replicate 1", "hypo1", null, null, null, null, null, null, null, null, null, null, "dataset for sample hypo1", "Seq7", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, null, null, 1111534488.0, 15437979.0, "hypo1 run1", "0:36 1:36", "A:273016370;C:277718934;G:279150260;T:281380668;N:268256", 36, 36, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae exposed to hypoxia stress replicate 1", "hypo1", null, null, null, null, null, null, null, null, null, null, "dataset for sample hypo1", "Seq7", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, "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, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae exposed to cold stress replicate 3", "cold3", null, null, null, null, null, null, null, null, null, null, "dataset for sample cold3", "Seq6", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, "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, null, null, 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", null, "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.", null, null, "1", "zebrafish larvae exposed to cold stress replicate 3", "cold3", null, null, null, null, null, null, null, null, null, null, "dataset for sample cold3", "Seq6", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "720Application ReadForward11Application ReadReverse37", "SRP017563", null, null, null, null, 912477384.0, 12673297.0, "cold3 run2", "0:36 1:36", "A:216126045;C:233918163;G:238615002;T:222532152;N:1286022", 36, 36, null, null, 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", null, "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 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