{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_selection = \"Oligo-dT\" and tissue_curation = \"Undetermined\"", "rows": [[312, "ERR977399", "ERX1054382", "ERS805483", "ERP011343", "PRJEB10137", "RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48", "Other", "Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal \u2013 non diabetic \u2013 animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.", null, null, null, "Ductal cells R3", "SAMEA3498334", "GIGA-R, University of Liege", "ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498334|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:3|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:3|strain:Tgnkx6.1:GPF", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 3", "unspecified", "1", "nextera XT", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011343", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16", "NGS14-B703_nkx2_TCCTGAGC_L003_R1_001.fastq.gz NGS14-B703_nkx2_TCCTGAGC_L003_R2_001.fastq.gz", "fastq fastq", 14253683247.0, 70913847.0, "ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 3", "0:101 1:100", "A:3767730088;C:2759135663;G:2772107550;T:3905748607;N:1048961339", 101, 100, null, null, 3767730088, 2759135663, 2772107550, 3905748607, 1048961339, "ERX1054382", "ERS805483", "ERA463457", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.74612, 0.7459, 0.10937, 0.11122, 0.81704, 0.81913, 0.54841, 0.53764, 101, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [313, "ERR977398", "ERX1054381", "ERS805482", "ERP011343", "PRJEB10137", "RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48", "Other", "Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal \u2013 non diabetic \u2013 animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.", null, null, null, "Ductal cells R2", "SAMEA3498333", "GIGA-R, University of Liege", "ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498333|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:2|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:2|strain:Tgnkx6.1:GPF", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 2", "unspecified", "1", "Truseq nano DNAsample", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011343", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16", "NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R2_001.fastq.gz NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R1_001.fastq.gz", "fastq fastq", 17434323262.0, 86308531.0, "ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 2", "0:101 1:101", "A:5014046305;C:3245710338;G:3382410145;T:5701198546;N:90957928", 101, 101, null, null, 5014046305, 3245710338, 3382410145, 5701198546, 90957928, "ERX1054381", "ERS805482", "ERA463457", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.87938, 0.83068, 0.30659, 0.31351, 0.80162, 0.8438, 0.50285, 0.47987, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [314, "ERR977397", "ERX1054380", "ERS805481", "ERP011343", "PRJEB10137", "RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48", "Other", "Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal \u2013 non diabetic \u2013 animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.", null, null, null, "Ductal cells R1", "SAMEA3498332", "GIGA-R, University of Liege", "ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498332|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:1|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:1|strain:Tgnkx6.1:GPF", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 1", "unspecified", "1", "Truseq nano DNA sample", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011343", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16", "NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R1_001.fastq.gz NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R2_001.fastq.gz", "fastq fastq", 8147922500.0, 40336250.0, "ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 1", "0:101 1:101", "A:2422471356;C:1435392327;G:1491979725;T:2755195660;N:42883432", 101, 101, null, null, 2422471356, 1435392327, 1491979725, 2755195660, 42883432, "ERX1054380", "ERS805481", "ERA463457", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.85302, 0.79849, 0.41437, 0.41711, 0.83871, 0.87012, 0.48354, 0.50046, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [315, "ERR1675931", "ERX1745976", "ERS805781", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R2 1", "SAMEA3498632", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498632|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:37|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:37", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 06 10 2016 15:53:35:325 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "A028_tefa_acinar_GTCCGC_L006_R1_001.fastq.gz A028_tefa_acinar_GTCCGC_L006_R2_001.fastq.gz", "fastq fastq", 10323596830.0, 51106915.0, "ena RUN GIGA R  University of Liege 06 10 2016 15:53:35:325 1", "0:101 1:101", "A:2531431314;C:2448656972;G:2434247998;T:2833404838;N:75855708", 101, 101, null, null, 2531431314, 2448656972, 2434247998, 2833404838, 75855708, "ERX1745976", "ERS805781", "ERA727496", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.86878, 0.78451, 0.03164, 0.02157, 0.95077, 0.96161, 0.52068, 0.26664, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [316, "ERR977594", "ERX1054577", "ERS805784", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R4", "SAMEA3498635", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498635|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:40|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:40", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 19", "Acinar R4", "1", "Truseq nano DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "NGS14-B702_Acinar4_GTGAAA_L008_R1_001.fastq.gz NGS14-B702_Acinar4_GTGAAA_L008_R2_001.fastq.gz", "fastq fastq", 16935208936.0, 83837668.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 19", "0:101 1:101", "A:4069193994;C:3974803883;G:4029409265;T:4779969672;N:81832122", 101, 101, null, null, 4069193994, 3974803883, 4029409265, 4779969672, 81832122, "ERX1054577", "ERS805784", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.93976, 0.89939, 0.01468, 0.01416, 0.93801, 0.94795, 0.50718, 0.50041, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [317, "ERR977593", "ERX1054576", "ERS805783", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R3", "SAMEA3498634", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498634|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:39|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:39", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 18", "Acinar R3", "1", "Truseq nano DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "NGS14-B701_Acinar3_ACAGTG_L008_R1_001.fastq.gz NGS14-B701_Acinar3_ACAGTG_L008_R2_001.fastq.gz", "fastq fastq", 15710260534.0, 77773567.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 18", "0:101 1:101", "A:3788172647;C:3700546898;G:3749520213;T:4395516227;N:76504549", 101, 101, null, null, 3788172647, 3700546898, 3749520213, 4395516227, 76504549, "ERX1054576", "ERS805783", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.95517, 0.92587, 0.0153, 0.01529, 0.91504, 0.92553, 0.49096, 0.48449, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [318, "ERR977592", "ERX1054575", "ERS805782", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R2 2", "SAMEA3498633", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498633|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:38|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:38", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 17", "Acinar R2 2", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "Acinar_A028_GTCCGC_L003_R1_001.fastq.gz Acinar_A028_GTCCGC_L003_R2_001.fastq.gz", "fastq fastq", 3461595220.0, 17136610.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 17", "0:101 1:101", "A:847745846;C:824702298;G:830498571;T:958264119;N:384386", 101, 101, null, null, 847745846, 824702298, 830498571, 958264119, 384386, "ERX1054575", "ERS805782", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.86246, 0.7781, 0.03038, 0.02178, 0.95357, 0.96327, 0.56719, 0.35588, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [319, "ERR977591", "ERX1054574", "ERS805780", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R1 2", "SAMEA3498631", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498631|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:36|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:36", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 16", "Acinar R1 2", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "Exocrine_GTGAAA_L005_R1_001.fastq.gz Exocrine_GTGAAA_L005_R2_001.fastq.gz", "fastq fastq", 9528535334.0, 47170967.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 16", "0:101 1:101", "A:2522050794;C:2076658898;G:2097686086;T:2672752253;N:159387303", 101, 101, null, null, 2522050794, 2076658898, 2097686086, 2672752253, 159387303, "ERX1054574", "ERS805780", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.48352, 0.37495, 0.01258, 0.01002, 0.94194, 0.95345, 0.51746, 0.51938, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [320, "ERR977590", "ERX1054573", "ERS805779", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Acinar cells from adults purified by FACS", "Acinar cells R1 1", "SAMEA3498630", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498630|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:35|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:35", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 15", "Acinar R1 1", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "Exocrine_30000_GTGAAA_L008_R1_001.fastq.gz Exocrine_30000_GTGAAA_L008_R2_001.fastq.gz", "fastq fastq", 2352127188.0, 11644194.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 15", "0:101 1:101", "A:575791638;C:562486325;G:570096367;T:643677230;N:75628", 101, 101, null, null, 575791638, 562486325, 570096367, 643677230, 75628, "ERX1054573", "ERS805779", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.96358, 0.92791, 0.02614, 0.02577, 0.91534, 0.92786, 0.51791, 0.51855, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [322, "ERR977588", "ERX1054571", "ERS805777", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Delta cells from adults purified by FACS", "Delta cells R2", "SAMEA3498628", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498628|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:33|cell type:Pancreatic Delta cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:33", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 13", "Delta R2", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "STS2_cDNA_A085_CAGATC_L003_R1_001.fastq.gz STS2_cDNA_A085_CAGATC_L003_R2_001.fastq.gz", "fastq fastq", 9070241774.0, 44902187.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 13", "0:101 1:101", "A:2535637917;C:1854694115;G:1908489704;T:2770396981;N:1023057", 101, 101, null, null, 2535637917, 1854694115, 1908489704, 2770396981, 1023057, "ERX1054571", "ERS805777", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.94245, 0.86716, 0.11229, 0.13234, 0.76114, 0.78171, 0.38511, 0.43811, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [323, "ERR977587", "ERX1054570", "ERS805776", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Delta cells from adults purified by FACS", "Delta cells R1 2", "SAMEA3498627", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498627|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:32|cell type:Pancreatic Delta cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:32", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 12", "Delta R1 2", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "SST1_A027_CCGTCC_L004_R1_001.fastq.gz SST1_A027_CCGTCC_L004_R2_001.fastq.gz", "fastq fastq", 7937290636.0, 39293518.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 12", "0:101 1:101", "A:2179525147;C:1634082904;G:1676353742;T:2446333583;N:995260", 101, 101, null, null, 2179525147, 1634082904, 1676353742, 2446333583, 995260, "ERX1054570", "ERS805776", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.81928, 0.64028, 0.09426, 0.0961, 0.80626, 0.83763, 0.33992, 0.39097, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [324, "ERR977586", "ERX1054569", "ERS805775", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Delta cells from adults purified by FACS", "Delta cells R1 1", "SAMEA3498626", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498626|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:31|cell type:Pancreatic Delta cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:31", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 11", "Delta R1 1", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "SST_CCGTCC_L005_R1_001.fastq.gz SST_CCGTCC_L005_R2_001.fastq.gz", "fastq fastq", 2808424382.0, 13903091.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 11", "0:101 1:101", "A:745970072;C:575317830;G:590596279;T:849527061;N:47013140", 101, 101, null, null, 745970072, 575317830, 590596279, 849527061, 47013140, "ERX1054569", "ERS805775", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.80308, 0.60403, 0.09111, 0.08841, 0.80582, 0.84035, 0.34177, 0.38788, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [325, "ERR977585", "ERX1054568", "ERS805774", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Alpha cells from adults purified by FACS", "Alpha cells R3", "SAMEA3498625", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498625|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:30|cell type:Pancreatic Alpha cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:30", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 10", "Alpha R3", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R1_001.fastq.gz NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R2_001.fastq.gz", "fastq fastq", 18205394430.0, 90125715.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 10", "0:101 1:101", "A:5028541426;C:3813667922;G:3871329588;T:5386457109;N:105398385", 101, 101, null, null, 5028541426, 3813667922, 3871329588, 5386457109, 105398385, "ERX1054568", "ERS805774", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.84473, 0.83714, 0.12924, 0.13497, 0.76581, 0.77928, 0.43397, 0.42534, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [326, "ERR977584", "ERX1054567", "ERS805773", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Alpha cells from adults purified by FACS", "Alpha cells R2 2", "SAMEA3498624", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498624|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:29|cell type:Pancreatic Alpha cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:29", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 9", "Alpha R2 2", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "A084_Alpha2cDNA_GCCAAT_L006_R1_001.fastq.gz A084_Alpha2cDNA_GCCAAT_L006_R2_001.fastq.gz", "fastq fastq", 8621351314.0, 42679957.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 9", "0:101 1:101", "A:2420008540;C:1748459249;G:1778002039;T:2610255006;N:64626480", 101, 101, null, null, 2420008540, 1748459249, 1778002039, 2610255006, 64626480, "ERX1054567", "ERS805773", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.8123, 0.7894, 0.13948, 0.14682, 0.76609, 0.78624, 0.43594, 0.4281, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [327, "ERR977583", "ERX1054566", "ERS805772", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Alpha cells from adults purified by FACS", "Alpha cells R2 1", "SAMEA3498623", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498623|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:28|cell type:Pancreatic Alpha cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:28", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 8", "Alpha R2 1", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "Alpha_2_cDNA_A084_GCCAAT_L003_R1_001.fastq.gz Alpha_2_cDNA_A084_GCCAAT_L003_R2_001.fastq.gz", "fastq fastq", 7447261462.0, 36867631.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 8", "0:101 1:101", "A:2085646680;C:1521470549;G:1568678066;T:2270630726;N:835441", 101, 101, null, null, 2085646680, 1521470549, 1568678066, 2270630726, 835441, "ERX1054566", "ERS805772", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.81689, 0.79405, 0.13796, 0.14503, 0.76583, 0.78535, 0.40729, 0.42815, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [328, "ERR977582", "ERX1054565", "ERS805771", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Alpha cells from adults purified by FACS", "Alpha cells R1 2", "SAMEA3498622", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498622|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:27|cell type:Pancreatic Alpha cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:27", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 7", "Alpha R1 2", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "A083_Alpha1cDNA_ACAGTG_L006_R1_001.fastq.gz A083_Alpha1cDNA_ACAGTG_L006_R2_001.fastq.gz", "fastq fastq", 8598483904.0, 42566752.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 7", "0:101 1:101", "A:2424152802;C:1756999772;G:1780718036;T:2571949581;N:64663713", 101, 101, null, null, 2424152802, 1756999772, 1780718036, 2571949581, 64663713, "ERX1054565", "ERS805771", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.80654, 0.78693, 0.13676, 0.14263, 0.76475, 0.78173, 0.4476, 0.44884, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [329, "ERR977581", "ERX1054564", "ERS805770", "ERP011346", "PRJEB10140", "RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish", "ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55", "Other", "We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   \u00df  and d cells as well as exocrine acinar and ductal cells.", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31", null, "Alpha cells from adults purified by FACS", "Alpha cells R1 1", "SAMEA3498621", "GIGA-R, University of Liege", "ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498621|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:26|cell type:Pancreatic Alpha cells|collected by:Estefania Tarife\u00f1o Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:26|strain:Tggcga:GFP; Tgins:NTR mCherry", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 6", "Alpha R1 1", "1", "Truseq DNA Sample prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP011346", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16", "Alpha1_cDNA_A083_ACAGTG_L003_R2_001.fastq.gz Alpha1_cDNA_A083_ACAGTG_L003_R1_001.fastq.gz", "fastq fastq", 7584054852.0, 37544826.0, "ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 6", "0:101 1:101", "A:2134120600;C:1561394450;G:1604139016;T:2283553056;N:847730", 101, 101, null, null, 2134120600, 1561394450, 1604139016, 2283553056, 847730, "ERX1054564", "ERS805770", "ERA463595", "GIGA-R, University of Liege|European Nucleotide Archive", "GIGA-R, University of Liege", 2, 0.8102, 0.79183, 0.13509, 0.1414, 0.76459, 0.77958, 0.44897, 0.42232, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2015-08-05", "Adult", "Adult", "Undetermined", "Undetermined"], [9951, "ERR5961093", "ERX5601614", "ERS6490233", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the same batch.", "Uninjected2", "Uninjected2", null, "ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 8", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14", null, null, null, null, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 8", null, null, null, null, null, null, null, null, null, null, null, "ERX5601614", null, "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9952, "ERR5961092", "ERX5601613", "ERS6490232", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the same batch.", "Uninjected1", "SAMEA8805898", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 06 23|ENA last update:2021 06 23|External Id:SAMEA8805898|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 06 23T08:18:31Z|INSDC last update:2021 06 23T08:18:31Z|INSDC status:public|Submitter Id:Uninjected1|common name:zebrafish|sample name:Uninjected1", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 7", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 06 23|ENA LAST UPDATE:2021 06 23", "WT1_R1_001.fastq WT1_R2_001.fastq", "fastq fastq", 5664550800.0, 18881836.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 7", "0:150 1:150", "A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763", 150, 150, null, null, 1493322675, 1337347146, 1388414458, 1444981758, 484763, "ERX5601613", "ERS6490232", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95769, 0.95822, 0.04407, 0.04391, 0.69934, 0.69958, 0.4411, 0.45319, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9953, "ERR5961096", "ERX5601617", "ERS6490236", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the an additional batch.", "Uninjected5", "SAMEA8805902", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805902|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected5|common name:zebrafish|sample name:Uninjected5", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 11", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "WT5_R1_001.fastq.gz WT5_R2_001.fastq.gz", "fastq fastq", 9088444200.0, 30294814.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 11", "0:150 1:150", "A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622", 150, 150, null, null, 2404715160, 2098546919, 2330441921, 2254532578, 207622, "ERX5601617", "ERS6490236", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95076, 0.93857, 0.06296, 0.06222, 0.68485, 0.70047, 0.47429, 0.48524, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9954, "ERR5961095", "ERX5601616", "ERS6490235", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the an additional batch.", "Uninjected4", "SAMEA8805901", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805901|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected4|common name:zebrafish|sample name:Uninjected4", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 10", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "WT4_R1_001.fastq.gz WT4_R2_001.fastq.gz", "fastq fastq", 9222083700.0, 30740279.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 10", "0:150 1:150", "A:2328864269;C:2117919914;G:2560286870;T:2214801519;N:211128", 150, 150, null, null, 2328864269, 2117919914, 2560286870, 2214801519, 211128, "ERX5601616", "ERS6490235", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95124, 0.92695, 0.05122, 0.05036, 0.69118, 0.70634, 0.47769, 0.47806, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9955, "ERR5961094", "ERX5601615", "ERS6490234", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae uninjected controls from the an additional batch.", "Uninjected3", "SAMEA8805900", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805900|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected3|common name:zebrafish|sample name:Uninjected3", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 9", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "WT3_R1_001.fastq.gz WT3_R2_001.fastq.gz", "fastq fastq", 9088444200.0, 30294814.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 9", "0:150 1:150", "A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622", 150, 150, null, null, 2404715160, 2098546919, 2330441921, 2254532578, 207622, "ERX5601615", "ERS6490234", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95071, 0.93855, 0.06295, 0.06183, 0.68511, 0.70065, 0.47621, 0.48573, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9956, "ERR5961091", "ERX5601612", "ERS6490231", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.", "Cas9enzyme3", "SAMEA8805897", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805897|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme3|common name:zebrafish|sample name:Cas9enzyme3", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "RNA3_R1_001.fastq RNA3_R2_001.fastq", "fastq fastq", 5814764400.0, 19382548.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 6", "0:150 1:150", "A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867", 150, 150, null, null, 1550014255, 1359566801, 1419514658, 1485169819, 498867, "ERX5601612", "ERS6490231", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.96166, 0.96182, 0.04962, 0.04954, 0.68172, 0.68144, 0.45683, 0.46611, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9957, "ERR5961090", "ERX5601611", "ERS6490230", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.", "Cas9enzyme2", "SAMEA8805896", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805896|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme2|common name:zebrafish|sample name:Cas9enzyme2", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "RNA2_R1_001.fastq RNA2_R2_001.fastq", "fastq fastq", 5927606100.0, 19758687.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 5", "0:150 1:150", "A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534", 150, 150, null, null, 1579767222, 1387675810, 1439122138, 1520529396, 511534, "ERX5601611", "ERS6490230", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.96217, 0.96214, 0.05174, 0.05176, 0.67083, 0.6716, 0.46772, 0.47128, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9958, "ERR5961089", "ERX5601610", "ERS6490229", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.", "Cas9enzyme1", "SAMEA8805895", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805895|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme1|common name:zebrafish|sample name:Cas9enzyme1", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "RNA1_R1_001.fastq RNA1_R2_001.fastq", "fastq fastq", 5738133000.0, 19127110.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 4", "0:150 1:150", "A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691", 150, 150, null, null, 1530616107, 1342298453, 1401357126, 1463360623, 500691, "ERX5601610", "ERS6490229", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95709, 0.9569, 0.05132, 0.05149, 0.68771, 0.68846, 0.45988, 0.47329, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9959, "ERR5961088", "ERX5601609", "ERS6490228", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.", "Cas9mRNA3", "SAMEA8805894", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805894|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA3|common name:zebrafish|sample name:Cas9mRNA3", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "PRO3_R1_001.fastq PRO3_R2_001.fastq", "fastq fastq", 9635841900.0, 32119473.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 3", "0:150 1:150", "A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911", 150, 150, null, null, 2562857735, 2253487693, 2325345541, 2493627020, 523911, "ERX5601609", "ERS6490228", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95769, 0.95696, 0.05441, 0.05397, 0.67424, 0.67407, 0.46338, 0.46444, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9960, "ERR5961087", "ERX5601608", "ERS6490227", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.", "Cas9mRNA2", "SAMEA8805893", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805893|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA2|common name:zebrafish|sample name:Cas9mRNA2", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 10 21", "PRO2_R1_001.fastq PRO2_R2_001.fastq", "fastq fastq", 8990649900.0, 29968833.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 2", "0:150 1:150", "A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619", 150, 150, null, null, 2370044440, 2140400380, 2185347925, 2294361536, 495619, "ERX5601608", "ERS6490227", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95444, 0.95397, 0.05839, 0.05842, 0.67377, 0.67207, 0.48505, 0.48043, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9961, "ERR5961086", "ERX5601607", "ERS6490226", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.", "Cas9mRNA1", "SAMEA8805892", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805892|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA1|common name:zebrafish|sample name:Cas9mRNA1", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP123184", "Illumina HiSeq 4000 paired end sequencing", "ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26", "PRO1_R1_001.fastq PRO1_R2_001.fastq", "fastq fastq", 8803789500.0, 29345965.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 1", "0:150 1:150", "A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952", 150, 150, null, null, 2318913314, 2090675347, 2149054140, 2244296747, 849952, "ERX5601607", "ERS6490226", "ERA4417635", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.954, 0.9549, 0.04652, 0.04639, 0.70806, 0.71386, 0.45393, 0.44921, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9962, "ERR4902960", "ERX4769932", "ERS5427208", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected.", "CRISPR RNAseq", "SAMEA7670216", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670216|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:12Z|INSDC status:public|Submitter Id:CRISPR RNAseq8|common name:zebrafish|sample name:CRISPR RNAseq8", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 8", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "WT2_R1_001.fastq.gz WT2_R2_001.fastq.gz", "fastq fastq", 7020700500.0, 23402335.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 8", "0:150 1:150", "A:1879937256;C:1626166066;G:1693802223;T:1820178560;N:616395", 150, 150, null, null, 1879937256, 1626166066, 1693802223, 1820178560, 616395, "ERX4769932", "ERS5427208", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.92352, 0.92388, 0.04778, 0.04768, 0.6924, 0.69205, 0.45557, 0.45865, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9963, "ERR4902959", "ERX4769931", "ERS5427206", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected.", "CRISPR RNAseq", "SAMEA7670214", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670214|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq7|common name:zebrafish|sample name:CRISPR RNAseq7", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 7", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "WT1_R1_001.fastq.gz WT1_R2_001.fastq.gz", "fastq fastq", 5664550800.0, 18881836.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 7", "0:150 1:150", "A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763", 150, 150, null, null, 1493322675, 1337347146, 1388414458, 1444981758, 484763, "ERX4769931", "ERS5427206", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95767, 0.95821, 0.04411, 0.04384, 0.69944, 0.69944, 0.44168, 0.45263, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9964, "ERR4902958", "ERX4769930", "ERS5427204", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.", "CRISPR RNAseq", "SAMEA7670212", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670212|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq6|common name:zebrafish|sample name:CRISPR RNAseq6", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "RNA3_R1_001.fastq.gz RNA3_R2_001.fastq.gz", "fastq fastq", 5814764400.0, 19382548.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 6", "0:150 1:150", "A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867", 150, 150, null, null, 1550014255, 1359566801, 1419514658, 1485169819, 498867, "ERX4769930", "ERS5427204", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.96165, 0.96177, 0.04961, 0.04952, 0.68183, 0.68142, 0.45636, 0.46565, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9965, "ERR4902957", "ERX4769929", "ERS5427203", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.", "CRISPR RNAseq", "SAMEA7670211", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670211|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq5|common name:zebrafish|sample name:CRISPR RNAseq5", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "RNA2_R1_001.fastq.gz RNA2_R2_001.fastq.gz", "fastq fastq", 5927606100.0, 19758687.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 5", "0:150 1:150", "A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534", 150, 150, null, null, 1579767222, 1387675810, 1439122138, 1520529396, 511534, "ERX4769929", "ERS5427203", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.96212, 0.96213, 0.0519, 0.05167, 0.67099, 0.6715, 0.46875, 0.47089, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9966, "ERR4902956", "ERX4769928", "ERS5427201", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.", "CRISPR RNAseq", "SAMEA7670209", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670209|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq4|common name:zebrafish|sample name:CRISPR RNAseq4", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "RNA1_R1_001.fastq.gz RNA1_R2_001.fastq.gz", "fastq fastq", 5738133000.0, 19127110.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 4", "0:150 1:150", "A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691", 150, 150, null, null, 1530616107, 1342298453, 1401357126, 1463360623, 500691, "ERX4769928", "ERS5427201", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95706, 0.9569, 0.05122, 0.05151, 0.68757, 0.68822, 0.46039, 0.4732, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9967, "ERR4902955", "ERX4769927", "ERS5427199", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.", "CRISPR RNAseq", "SAMEA7670207", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670207|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq3|common name:zebrafish|sample name:CRISPR RNAseq3", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "PRO3_R1_001.fastq.gz PRO3_R2_001.fastq.gz", "fastq fastq", 9635841900.0, 32119473.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 3", "0:150 1:150", "A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911", 150, 150, null, null, 2562857735, 2253487693, 2325345541, 2493627020, 523911, "ERX4769927", "ERS5427199", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95766, 0.95695, 0.05445, 0.05404, 0.67432, 0.67403, 0.46385, 0.46442, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9968, "ERR4902954", "ERX4769926", "ERS5427197", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.", "CRISPR RNAseq", "SAMEA7670205", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670205|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq2|common name:zebrafish|sample name:CRISPR RNAseq2", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "PRO2_R1_001.fastq.gz PRO2_R2_001.fastq.gz", "fastq fastq", 8990649900.0, 29968833.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 2", "0:150 1:150", "A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619", 150, 150, null, null, 2370044440, 2140400380, 2185347925, 2294361536, 495619, "ERX4769926", "ERS5427197", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95444, 0.95393, 0.05848, 0.05894, 0.67438, 0.67255, 0.4825, 0.48028, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [9969, "ERR4902953", "ERX4769925", "ERS5427195", "ERP123184", "PRJEB39643", "CRISPR tools for zebrafish", "ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095", "Other", "Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.", "ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25", null, "RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.", "CRISPR RNAseq", "SAMEA7670203", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670203|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq1|common name:zebrafish|sample name:CRISPR RNAseq1", null, null, null, null, null, null, null, null, "Illumina MiSeq paired end sequencing", "ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "ERP123184", "Illumina MiSeq paired end sequencing", "ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09", "PRO1_R1_001.fastq.gz PRO1_R2_001.fastq.gz", "fastq fastq", 8803789500.0, 29345965.0, "ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 1", "0:150 1:150", "A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952", 150, 150, null, null, 2318913314, 2090675347, 2149054140, 2244296747, 849952, "ERX4769925", "ERS5427195", "ERA3183786", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", 2, 0.95403, 0.95489, 0.04655, 0.0464, 0.70816, 0.71403, 0.45357, 0.44874, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-31", "Larval", "Larval", "Undetermined", "Undetermined"], [31825, "SRR28700412", "SRX24268115", "SRS21034395", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "PN 2", null, "isolate:PN2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "PN 2", "PN 2", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "PN_2_1.fq.gz PN_2_2.fq.gz", "fastq fastq", 6385048200.0, 21283494.0, "PN 2 1.fq.gz", "0:150 1:150", "A:1722127999;C:1463645587;G:1483173818;T:1716100796;N:0", 150, 150, null, null, 1722127999, 1463645587, 1483173818, 1716100796, 0, "SRX24268115", "SRS21034395", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31826, "SRR28700413", "SRX24268114", "SRS21034397", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "PN 1", null, "isolate:PN1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "PN 1", "PN 1", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "PN_1_1.fq.gz PN_1_2.fq.gz", "fastq fastq", 6692894100.0, 22309647.0, "PN 1 1.fq.gz", "0:150 1:150", "A:1827107021;C:1513034624;G:1533077624;T:1819674831;N:0", 150, 150, null, null, 1827107021, 1513034624, 1533077624, 1819674831, 0, "SRX24268114", "SRS21034397", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31827, "SRR28700414", "SRX24268113", "SRS21034396", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "EC 4", null, "isolate:EC4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "EC 4", "EC 4", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "EC_4_1.fq.gz EC_4_2.fq.gz", "fastq fastq", 6688857000.0, 22296190.0, "EC 4 1.fq.gz", "0:150 1:150", "A:1820989545;C:1516814697;G:1537970654;T:1813082104;N:0", 150, 150, null, null, 1820989545, 1516814697, 1537970654, 1813082104, 0, "SRX24268113", "SRS21034396", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31828, "SRR28700415", "SRX24268112", "SRS21034392", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "EC 3", null, "isolate:EC3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "EC 3", "EC 3", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "EC_3_1.fq.gz EC_3_2.fq.gz", "fastq fastq", 6696553800.0, 22321846.0, "EC 3 1.fq.gz", "0:150 1:150", "A:1821249100;C:1520587242;G:1541238550;T:1813478908;N:0", 150, 150, null, null, 1821249100, 1520587242, 1541238550, 1813478908, 0, "SRX24268112", "SRS21034392", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31829, "SRR28700416", "SRX24268111", "SRS21034391", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "EC 2", null, "isolate:EC2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "EC 2", "EC 2", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "EC_2_1.fq.gz EC_2_2.fq.gz", "fastq fastq", 6702179400.0, 22340598.0, "EC 2 1.fq.gz", "0:150 1:150", "A:1816692261;C:1527379142;G:1547365810;T:1810742187;N:0", 150, 150, null, null, 1816692261, 1527379142, 1547365810, 1810742187, 0, "SRX24268111", "SRS21034391", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31830, "SRR28700417", "SRX24268110", "SRS21034390", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "EC 1", null, "isolate:EC1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "EC 1", "EC 1", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "EC_1_1.fq.gz EC_1_2.fq.gz", "fastq fastq", 6686053500.0, 22286845.0, "EC 1 1.fq.gz", "0:150 1:150", "A:1812022780;C:1524359858;G:1544847441;T:1804823421;N:0", 150, 150, null, null, 1812022780, 1524359858, 1544847441, 1804823421, 0, "SRX24268110", "SRS21034390", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31831, "SRR28700418", "SRX24268109", "SRS21034388", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "Control 4", null, "isolate:con4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "Control 4", "Control 4", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "Control_4_1.fq.gz Control_4_2.fq.gz", "fastq fastq", 6669700500.0, 22232335.0, "Control 4 1.fq.gz", "0:150 1:150", "A:1804178265;C:1523547469;G:1543839484;T:1798135282;N:0", 150, 150, null, null, 1804178265, 1523547469, 1543839484, 1798135282, 0, "SRX24268109", "SRS21034388", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31832, "SRR28700419", "SRX24268108", "SRS21034387", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "Control 3", null, "isolate:con3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "Control 3", "Control 3", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "Control_3_1.fq.gz Control_3_2.fq.gz", "fastq fastq", 6683518800.0, 22278396.0, "Control 3 1.fq.gz", "0:150 1:150", "A:1808495506;C:1525725204;G:1545930043;T:1803368047;N:0", 150, 150, null, null, 1808495506, 1525725204, 1545930043, 1803368047, 0, "SRX24268108", "SRS21034387", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31833, "SRR28700420", "SRX24268107", "SRS21034386", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "PN 4", null, "isolate:PN4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "PN 4", "PN 4", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "PN_4_1.fq.gz PN_4_2.fq.gz", "fastq fastq", 6649316100.0, 22164387.0, "PN 4 1.fq.gz", "0:150 1:150", "A:1809816121;C:1508072480;G:1528272654;T:1803154845;N:0", 150, 150, null, null, 1809816121, 1508072480, 1528272654, 1803154845, 0, "SRX24268107", "SRS21034386", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31834, "SRR28700421", "SRX24268106", "SRS21034389", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "PN 3", null, "isolate:PN3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "PN 3", "PN 3", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "PN_3_1.fq.gz PN_3_2.fq.gz", "fastq fastq", 6616113900.0, 22053713.0, "PN 3 1.fq.gz", "0:150 1:150", "A:1802283686;C:1499008018;G:1519150002;T:1795672194;N:0", 150, 150, null, null, 1802283686, 1499008018, 1519150002, 1795672194, 0, "SRX24268106", "SRS21034389", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31835, "SRR28700422", "SRX24268105", "SRS21034385", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "Control 2", null, "isolate:con2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "Control 2", "Control 2", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "Control_2_1.fq.gz Control_2_2.fq.gz", "fastq fastq", 6701719200.0, 22339064.0, "Control 2 1.fq.gz", "0:150 1:150", "A:1812352260;C:1531672703;G:1551377072;T:1806317165;N:0", 150, 150, null, null, 1812352260, 1531672703, 1551377072, 1806317165, 0, "SRX24268105", "SRS21034385", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31836, "SRR28700423", "SRX24268104", "SRS21034384", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "Control 1", null, "isolate:con1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "Control 1", "Control 1", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "Control_1_1.fq.gz Control_1_2.fq.gz", "fastq fastq", 6720214500.0, 22400715.0, "Control 1 1.fq.gz", "0:150 1:150", "A:1814883015;C:1537948710;G:1559376116;T:1808006659;N:0", 150, 150, null, null, 1814883015, 1537948710, 1559376116, 1808006659, 0, "SRX24268104", "SRS21034384", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [33350, "SRR30136585", "SRX25605812", "SRS22254471", "SRP524293", "PRJNA1143173", "Toxic mechanism of the novel pesticide pyrifluquinazon PFQ and its major metabolite in early life stage zebrafish", "PRJNA1143173", "Other", "To investigate the mechanisms underlying the developmental toxicity of PFQ and dPFQ in zebrafish early life stage  RNA seq and transcriptomic analyses were conducted. For the solvent control  middle and high concentration groups of PFQ and dPFQ exposure  3 biological replicates were included  making 15 samples in total. The sequencing was performed by Novogene Co.  Ltd.  China.", null, null, "14", null, "01H2", null, "strain:WILD|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:larvae|collection date:2022 11 20|geo loc name:China|sex:not determined|tissue:larvae|replicate:dPFQ H replicate biological 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of daniorerio", "01H2", "01H2", "Illumina NovaSeq 6000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP524293", null, null, "01H2_1.fq.gz 01H2_2.fq.gz", "fastq fastq", 6313056900.0, 21043523.0, "01H2 1.fq.gz", "0:150 1:150", "A:1766006943;C:1407384164;G:1393123543;T:1746425506;N:116744", 150, 150, null, null, 1766006943, 1407384164, 1393123543, 1746425506, 116744, "SRX25605812", "SRS22254471", "SRA1939705", "Research Center for Eco-Environmental Sciences|University of Chinese Academy of Sciences", "Research Center for Eco-Environmental Sciences", 2, 0.85886, 0.85703, 0.20363, 0.20144, 0.74044, 0.74249, 0.55406, 0.5549, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-08-05", "Larval", "Larval", "Undetermined", "Undetermined"], [35808, "SRR33047377", "SRX28312718", "SRS24651720", "SRP577472", "PRJNA1248424", "Danio rerio Raw sequence reads", "PRJNA1248424", "Whole Genome Sequencing", "The RNA seq of Danio rerio", null, null, null, null, "WT4", null, "breed:AB|age:16 days|collection date:2024 12 16|geo loc name:China:Zhuhai|sex:not determined|tissue:The round fish|genotype:wild type|replicate:biological replicate 4 in the control group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "WT4", "WT4", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP577472", null, null, "WT4_R1.fq.gz WT4_R2.fq.gz", "fastq fastq", 6933657000.0, 23112190.0, "WT4 R1.fq.gz", "0:150 1:150", "A:1937795555;C:1519113776;G:1563704738;T:1909641871;N:3401060", 150, 150, null, null, 1937795555, 1519113776, 1563704738, 1909641871, 3401060, "SRX28312718", "SRS24651720", "SRA2108999", "Sun Yat-sen University|Sun Yat-sen University", "Sun Yat-sen University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Undetermined", "Undetermined"], [35809, "SRR33047378", "SRX28312717", "SRS24651718", "SRP577472", "PRJNA1248424", "Danio rerio Raw sequence reads", "PRJNA1248424", "Whole Genome Sequencing", "The RNA seq of Danio rerio", null, null, null, null, "WT3", null, "breed:AB|age:16 days|collection date:2024 12 16|geo loc name:China:Zhuhai|sex:not determined|tissue:The round fish|genotype:wild type|replicate:biological replicate 3 in the control group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "WT3", "WT3", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP577472", null, null, "WT3_R1.fq.gz WT3_R2.fq.gz", "fastq fastq", 6956770500.0, 23189235.0, "WT3 R1.fq.gz", "0:150 1:150", "A:1955909582;C:1516895253;G:1552993746;T:1927330273;N:3641646", 150, 150, null, null, 1955909582, 1516895253, 1552993746, 1927330273, 3641646, "SRX28312717", "SRS24651718", "SRA2108999", "Sun Yat-sen University|Sun Yat-sen University", "Sun Yat-sen University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Undetermined", "Undetermined"], [35810, "SRR33047379", "SRX28312716", "SRS24651719", "SRP577472", "PRJNA1248424", "Danio rerio Raw sequence reads", "PRJNA1248424", "Whole Genome Sequencing", "The RNA seq of Danio rerio", null, null, null, null, "WT2", null, "breed:AB|age:16 days|collection date:2024 12 16|geo loc name:China:Zhuhai|sex:not determined|tissue:The round fish|genotype:wild type|replicate:biological replicate 2 in the control group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "WT2", "WT2", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP577472", null, null, "WT2_R1.fq.gz WT2_R2.fq.gz", "fastq fastq", 7505465100.0, 25018217.0, "WT2 R1.fq.gz", "0:150 1:150", "A:2101883253;C:1645411197;G:1682739575;T:2071755705;N:3675370", 150, 150, null, null, 2101883253, 1645411197, 1682739575, 2071755705, 3675370, "SRX28312716", "SRS24651719", "SRA2108999", "Sun Yat-sen University|Sun Yat-sen University", "Sun Yat-sen University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Undetermined", "Undetermined"], [35811, "SRR33047380", "SRX28312715", "SRS24651717", "SRP577472", "PRJNA1248424", "Danio rerio Raw sequence reads", "PRJNA1248424", "Whole Genome Sequencing", "The RNA seq of Danio rerio", null, null, null, null, "WT1", null, "breed:AB|age:16 days|collection date:2024 12 16|geo loc name:China:Zhuhai|sex:not determined|tissue:The round fish|genotype:wild type|replicate:biological replicate 1 in the control group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "WT1", "WT1", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP577472", null, null, "WT1_R1.fq.gz WT1_R2.fq.gz", "fastq fastq", 6841214400.0, 22804048.0, "WT1 R1.fq.gz", "0:150 1:150", "A:1920228684;C:1499116256;G:1529226612;T:1889060147;N:3582701", 150, 150, null, null, 1920228684, 1499116256, 1529226612, 1889060147, 3582701, "SRX28312715", "SRS24651717", "SRA2108999", "Sun Yat-sen University|Sun Yat-sen University", "Sun Yat-sen University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Undetermined", "Undetermined"], [35812, "SRR33047381", "SRX28312714", "SRS24651715", "SRP577472", "PRJNA1248424", "Danio rerio Raw sequence reads", "PRJNA1248424", "Whole Genome Sequencing", "The RNA seq of Danio rerio", null, null, null, null, "ACE4", null, "breed:AB|age:16 days|collection date:2024 12 16|geo loc name:China:Zhuhai|sex:not determined|tissue:The round fish|genotype:ace  / |replicate:biological replicate 4 in the mutate group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "ACE4", "ACE4", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP577472", null, null, "AC4_R1.fq.gz AC4_R2.fq.gz", "fastq fastq", 6850158300.0, 22833861.0, "AC4 R1.fq.gz", "0:150 1:150", "A:1898072939;C:1518842682;G:1559008533;T:1871496075;N:2738071", 150, 150, null, null, 1898072939, 1518842682, 1559008533, 1871496075, 2738071, "SRX28312714", "SRS24651715", "SRA2108999", "Sun Yat-sen University|Sun Yat-sen University", "Sun Yat-sen University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Undetermined", "Undetermined"], [35813, "SRR33047382", "SRX28312713", "SRS24651714", "SRP577472", "PRJNA1248424", "Danio rerio Raw sequence reads", "PRJNA1248424", "Whole Genome Sequencing", "The RNA seq of Danio rerio", null, null, null, null, "ACE3", null, "breed:AB|age:16 days|collection date:2024 12 16|geo loc name:China:Zhuhai|sex:not determined|tissue:The round fish|genotype:ace  / |replicate:biological replicate 3 in the mutate group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "ACE3", "ACE3", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP577472", null, null, "AC3_R1.fq.gz AC3_R2.fq.gz", "fastq fastq", 6562714500.0, 21875715.0, "AC3 R1.fq.gz", "0:150 1:150", "A:1810600301;C:1455285126;G:1501234399;T:1792186624;N:3408050", 150, 150, null, null, 1810600301, 1455285126, 1501234399, 1792186624, 3408050, "SRX28312713", "SRS24651714", "SRA2108999", "Sun Yat-sen University|Sun Yat-sen University", "Sun Yat-sen University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Undetermined", "Undetermined"], [35814, "SRR33047383", "SRX28312712", "SRS24651716", "SRP577472", "PRJNA1248424", "Danio rerio Raw sequence reads", "PRJNA1248424", "Whole Genome Sequencing", "The RNA seq of Danio rerio", null, null, null, null, "ACE2", null, "breed:AB|age:16 days|collection date:2024 12 16|geo loc name:China:Zhuhai|sex:not determined|tissue:The round fish|genotype:ace  / |replicate:biological replicate 2 in the mutate group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "ACE2", "ACE2", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP577472", null, null, "AC2_R1.fq.gz AC2_R2.fq.gz", "fastq fastq", 7103182200.0, 23677274.0, "AC2 R1.fq.gz", "0:150 1:150", "A:1984084187;C:1557222983;G:1597912123;T:1960203230;N:3759677", 150, 150, null, null, 1984084187, 1557222983, 1597912123, 1960203230, 3759677, "SRX28312712", "SRS24651716", "SRA2108999", "Sun Yat-sen University|Sun Yat-sen University", "Sun Yat-sen University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Undetermined", "Undetermined"], [35815, "SRR33047384", "SRX28312711", "SRS24651712", "SRP577472", "PRJNA1248424", "Danio rerio Raw sequence reads", "PRJNA1248424", "Whole Genome Sequencing", "The RNA seq of Danio rerio", null, null, null, null, "ACE1", null, "breed:AB|age:16 days|collection date:2024 12 16|geo loc name:China:Zhuhai|sex:not determined|tissue:The round fish|genotype:ace  / |replicate:biological replicate 1 in the mutate group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "ACE1", "ACE1", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP577472", null, null, "AC1_R1.fq.gz AC1_R2.fq.gz", "fastq fastq", 7271149200.0, 24237164.0, "AC1 R1.fq.gz", "0:150 1:150", "A:2020364086;C:1600073941;G:1649953306;T:1996832193;N:3925674", 150, 150, null, null, 2020364086, 1600073941, 1649953306, 1996832193, 3925674, "SRX28312711", "SRS24651712", "SRA2108999", "Sun Yat-sen University|Sun Yat-sen University", "Sun Yat-sen University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Undetermined", "Undetermined"], [55643, "SRR10604044", "SRX7283593", "SRS5777402", "SRP235014", "PRJNA594101", "Danio rerio Transcriptome", "PRJNA594101", "Other", "Danio rerio Transcriptome post cGAS and STING knockout", null, null, null, null, "stko2", null, "strain:not collected|isolate:sting knockout 2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebraish larvae", "sting knockout 2", "sting knockout 2", "RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP235014", null, null, "stko2_1.fastq.gz stko2_2.fastq.gz", "fastq fastq", 10635609300.0, 70904062.0, "stko2 1.fastq.gz", "0:150 1:150", "A:2864931942;C:2450585568;G:2436540783;T:2882828480;N:722527", 150, 150, null, null, 2864931942, 2450585568, 2436540783, 2882828480, 722527, "SRX7283593", "SRS5777402", "SRA1007465", "Shantou university medical college|Neuroscience Center", "Shantou university medical college", 1, 0.93079, null, 0.07849, null, 0.70301, null, 0.47872, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-08", "Larval", "Larval", "Undetermined", "Undetermined"], [55644, "SRR10604045", "SRX7283592", "SRS5777401", "SRP235014", "PRJNA594101", "Danio rerio Transcriptome", "PRJNA594101", "Other", "Danio rerio Transcriptome post cGAS and STING knockout", null, null, null, null, "stko1", null, "strain:not collected|isolate:sting knockout 1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebraish larvae", "sting knockout 1", "sting knockout 1", "RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP235014", null, null, "stko1_1.fastq.gz stko1_2.fastq.gz", "fastq fastq", 10453959000.0, 69693060.0, "stko1 1.fastq.gz", "0:150 1:150", "A:2823253748;C:2400078679;G:2379662427;T:2850274552;N:689594", 150, 150, null, null, 2823253748, 2400078679, 2379662427, 2850274552, 689594, "SRX7283592", "SRS5777401", "SRA1007465", "Shantou university medical college|Neuroscience Center", "Shantou university medical college", 1, 0.92736, null, 0.08475, null, 0.69822, null, 0.47233, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-08", "Larval", "Larval", "Undetermined", "Undetermined"], [55645, "SRR10604046", "SRX7283591", "SRS5777400", "SRP235014", "PRJNA594101", "Danio rerio Transcriptome", "PRJNA594101", "Other", "Danio rerio Transcriptome post cGAS and STING knockout", null, null, null, null, "cgko2", null, "strain:not collected|isolate:cgas knockout 2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebraish larvae", "cgas knockout 2", "cgas knockout 2", "RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP235014", null, null, "cgko2_1.fastq.gz cgko2_2.fastq.gz", "fastq fastq", 10462236900.0, 69748246.0, "cgko2 1.fastq.gz", "0:150 1:150", "A:2836737922;C:2388112649;G:2370425883;T:2866326601;N:633845", 150, 150, null, null, 2836737922, 2388112649, 2370425883, 2866326601, 633845, "SRX7283591", "SRS5777400", "SRA1007465", "Shantou university medical college|Neuroscience Center", "Shantou university medical college", 1, 0.93603, null, 0.10606, null, 0.67765, null, 0.46153, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-08", "Larval", "Larval", "Undetermined", "Undetermined"], [55646, "SRR10604047", "SRX7283590", "SRS5777399", "SRP235014", "PRJNA594101", "Danio rerio Transcriptome", "PRJNA594101", "Other", "Danio rerio Transcriptome post cGAS and STING knockout", null, null, null, null, "cgko1", null, "strain:not collected|isolate:cgas knockout 1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebraish larvae", "cgas knockout 1", "cgas knockout 1", "RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP235014", null, null, "cgko1_2.fastq.gz cgko1_1.fastq.gz", "fastq fastq", 10498495500.0, 69989970.0, "cgko1 1.fastq.gz", "0:150 1:150", "A:2845684832;C:2398817161;G:2379300746;T:2874108573;N:584188", 150, 150, null, null, 2845684832, 2398817161, 2379300746, 2874108573, 584188, "SRX7283590", "SRS5777399", "SRA1007465", "Shantou university medical college|Neuroscience Center", "Shantou university medical college", 1, 0.93684, null, 0.10589, null, 0.67933, null, 0.48363, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-08", "Larval", "Larval", "Undetermined", "Undetermined"], [55647, "SRR10604048", "SRX7283589", "SRS5777398", "SRP235014", "PRJNA594101", "Danio rerio Transcriptome", "PRJNA594101", "Other", "Danio rerio Transcriptome post cGAS and STING knockout", null, null, null, null, "wt2", null, "strain:not collected|isolate:normal 2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebraish larvae", "wt normal 2", "wt normal 2", "RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP235014", null, null, "wt2_1.fastq.gz wt2_2.fastq.gz", "fastq fastq", 10660916400.0, 71072776.0, "wt2 1.fastq.gz", "0:150 1:150", "A:2906473511;C:2417423798;G:2405111864;T:2931146507;N:760720", 150, 150, null, null, 2906473511, 2417423798, 2405111864, 2931146507, 760720, "SRX7283589", "SRS5777398", "SRA1007465", "Shantou university medical college|Neuroscience Center", "Shantou university medical college", 1, 0.94167, null, 0.11781, null, 0.66831, null, 0.4757, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-08", "Larval", "Larval", "Undetermined", "Undetermined"], [55648, "SRR10604049", "SRX7283588", "SRS5777397", "SRP235014", "PRJNA594101", "Danio rerio Transcriptome", "PRJNA594101", "Other", "Danio rerio Transcriptome post cGAS and STING knockout", null, null, null, null, "wt1", null, "strain:not collected|isolate:normal 1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebraish larvae", "wt nomal 1", "wt nomal 1", "RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP235014", null, null, "wt1_1.fastq.gz wt1_2.fastq.gz", "fastq fastq", 10599804000.0, 70665360.0, "wt1 1.fastq.gz", "0:150 1:150", "A:2896989124;C:2397285811;G:2382705623;T:2922067937;N:755505", 150, 150, null, null, 2896989124, 2397285811, 2382705623, 2922067937, 755505, "SRX7283588", "SRS5777397", "SRA1007465", "Shantou university medical college|Neuroscience Center", "Shantou university medical college", 1, 0.93947, null, 0.11723, null, 0.67203, null, 0.45826, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-08", "Larval", "Larval", "Undetermined", "Undetermined"], [66966, "SRR16965145", "SRX13156590", "SRS11088493", "SRP346547", "PRJNA780808", "transcriptomics of carbendazim and enrofloxacin on zebrafish embryos", "PRJNA780808", "Other", "reveal a interaction between ENF and CAR on metabolic regulation during development", null, null, null, null, "1enf", null, "strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:7 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio :enrofloxacin group", "enf 1", "enf 1", "96hpf zebrafish larvae enrofloxacin group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP346547", null, null, "enf_1.fq.gz enf_2.fq.gz", "fastq fastq", 6652389300.0, 44349262.0, "enf 1.fq.gz", "0:150 1:150", "A:1759651033;C:1563446116;G:1556912596;T:1772370048;N:9507", 150, 150, null, null, 1759651033, 1563446116, 1556912596, 1772370048, 9507, "SRX13156590", "SRS11088493", "SRA1329868", "China Agricultural University|College of animal science and technology", "China Agricultural University", 1, 0.94992, null, 0.06316, null, 0.66979, null, 0.48987, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-11-17", "Larval", "Larval", "Undetermined", "Undetermined"], [66971, "SRR16965150", "SRX13156585", "SRS11088490", "SRP346547", "PRJNA780808", "transcriptomics of carbendazim and enrofloxacin on zebrafish embryos", "PRJNA780808", "Other", "reveal a interaction between ENF and CAR on metabolic regulation during development", null, null, null, null, "2mix", null, "strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:11 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio :mixture group", "mix 2", "mix 2", "96hpf zebrafish larvae mixture group", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP346547", null, null, "car_2_2.fq.gz mix2_2_1.fq.gz", "fastq fastq", 6669719100.0, 44464794.0, "car 2 2.fq.gz", "0:150 1:150", "A:1815824677;C:1515086864;G:1506360115;T:1832433148;N:14296", 150, 150, null, null, 1815824677, 1515086864, 1506360115, 1832433148, 14296, "SRX13156585", "SRS11088490", "SRA1329868", "China Agricultural University|College of animal science and technology", "China Agricultural University", 1, 0.93884, null, 0.11657, null, 0.65527, null, 0.48114, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-11-17", "Larval", "Larval", "Undetermined", "Undetermined"], [66974, "SRR16959538", "SRX13151074", "SRS11083380", "SRP346418", "PRJNA780940", "transcriptomics of difenoconazole and dimethomorph on zebrafish embryos", "PRJNA780940", "Other", "Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.", null, null, null, null, "1+mix", null, "strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:10 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : mixture group", "mix 1", "mix 1", "The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP346418", null, null, "mix1_3_2.fq.gz mix1_1_1.fq.gz", "fastq fastq", 6639699600.0, 44264664.0, "mix1 1 1.fq.gz", "0:150 1:150", "A:1738687157;C:1575344731;G:1569683716;T:1755974708;N:9288", 150, 150, null, null, 1738687157, 1575344731, 1569683716, 1755974708, 9288, "SRX13151074", "SRS11083380", "SRA1330365", "China Agricultural University|College of animal science and technology", "China Agricultural University", 1, 0.95161, null, 0.05697, null, 0.6817, null, 0.48485, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-11-16", "Larval", "Larval", "Undetermined", "Undetermined"], [66981, "SRR16959545", "SRX13151067", "SRS11083373", "SRP346418", "PRJNA780940", "transcriptomics of difenoconazole and dimethomorph on zebrafish embryos", "PRJNA780940", "Other", "Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.", null, null, null, null, "2+mix", null, "strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:11 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : mixture group", "mix 2", "mix 2", "The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP346418", null, null, "mix1_2_1.fq.gz dim_3_2.fq.gz", "fastq fastq", 6589866900.0, 43932446.0, "dim 3 2.fq.gz", "0:150 1:150", "A:1782755416;C:1508342477;G:1501934674;T:1796820276;N:14057", 150, 150, null, null, 1782755416, 1508342477, 1501934674, 1796820276, 14057, "SRX13151067", "SRS11083373", "SRA1330365", "China Agricultural University|College of animal science and technology", "China Agricultural University", 1, 0.93861, null, 0.10685, null, 0.66393, null, 0.47194, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-11-16", "Larval", "Larval", "Undetermined", "Undetermined"], [69921, "SRR19182974", "SRX15248102", "SRS12980685", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "Ni 100uM 3", null, "strain:not applicable|isolate:100uM Nickel exposure|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S982", "S982", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "Ni_100uM_3_1.fq.gz Ni_100uM_3_2.fq.gz", "fastq fastq", 7087256700.0, 23624189.0, "Ni 100uM 3 1.fq.gz", "0:150 1:150", "A:1847706912;C:1708802407;G:1702305397;T:1828359100;N:82884", 150, 150, null, null, 1847706912, 1708802407, 1702305397, 1828359100, 82884, "SRX15248102", "SRS12980685", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.96135, 0.96011, 0.03978, 0.03986, 0.66904, 0.66933, 0.49168, 0.49222, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [69922, "SRR19182975", "SRX15248101", "SRS12980683", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "Ni 100uM 2", null, "strain:not applicable|isolate:100uM Nickel exposure|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S981", "S981", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "Ni_100uM_2_1.fq.gz Ni_100uM_2_2.fq.gz", "fastq fastq", 7231767600.0, 24105892.0, "Ni 100uM 2 1.fq.gz", "0:150 1:150", "A:1860765489;C:1765825469;G:1761745224;T:1843343612;N:87806", 150, 150, null, null, 1860765489, 1765825469, 1761745224, 1843343612, 87806, "SRX15248101", "SRS12980683", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.9621, 0.96125, 0.0338, 0.03329, 0.67661, 0.67651, 0.49335, 0.49239, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [69923, "SRR19182976", "SRX15248100", "SRS12980682", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "Ni 100uM 1", null, "strain:not applicable|isolate:100uM Nickel exposure|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S980", "S980", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "Ni_100uM_1_1.fq.gz Ni_100uM_1_2.fq.gz", "fastq fastq", 6882243600.0, 22940812.0, "Ni 100uM 1 1.fq.gz", "0:150 1:150", "A:1772333382;C:1679182546;G:1676381144;T:1754273920;N:72608", 150, 150, null, null, 1772333382, 1679182546, 1676381144, 1754273920, 72608, "SRX15248100", "SRS12980682", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.96183, 0.9613, 0.03846, 0.03796, 0.66888, 0.6688, 0.48512, 0.50002, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [69924, "SRR19182977", "SRX15248099", "SRS12980681", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "Ni 10uM 3", null, "strain:not applicable|isolate:10uM Nickel exposure|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S979", "S979", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "Ni_10uM_3_1.fq.gz Ni_10uM_3_2.fq.gz", "fastq fastq", 6993378900.0, 23311263.0, "Ni 10uM 3 1.fq.gz", "0:150 1:150", "A:1795310290;C:1711834730;G:1710250417;T:1775904413;N:79050", 150, 150, null, null, 1795310290, 1711834730, 1710250417, 1775904413, 79050, "SRX15248099", "SRS12980681", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.96244, 0.96248, 0.03715, 0.03695, 0.6745, 0.67428, 0.48675, 0.48805, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [69925, "SRR19182978", "SRX15248098", "SRS12980680", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "Ni 10uM 2", null, "strain:not applicable|isolate:10uM Nickel exposure|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S978", "S978", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "Ni_10uM_2_1.fq.gz Ni_10uM_2_2.fq.gz", "fastq fastq", 8304187200.0, 27680624.0, "Ni 10uM 2 1.fq.gz", "0:150 1:150", "A:2136061361;C:2027545559;G:2026754522;T:2113739869;N:85889", 150, 150, null, null, 2136061361, 2027545559, 2026754522, 2113739869, 85889, "SRX15248098", "SRS12980680", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.96173, 0.96099, 0.04006, 0.03981, 0.67083, 0.67028, 0.48041, 0.47866, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [69926, "SRR19182979", "SRX15248097", "SRS12980684", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "Ni 10uM 1", null, "strain:not applicable|isolate:10uM Nickel exposure|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S977", "S977", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "Ni_10uM_1_1.fq.gz Ni_10uM_1_2.fq.gz", "fastq fastq", 7155178500.0, 23850595.0, "Ni 10uM 1 1.fq.gz", "0:150 1:150", "A:1843255719;C:1746501427;G:1737223211;T:1828109959;N:88184", 150, 150, null, null, 1843255719, 1746501427, 1737223211, 1828109959, 88184, "SRX15248097", "SRS12980684", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.96789, 0.96685, 0.04044, 0.04074, 0.67058, 0.67097, 0.49077, 0.49303, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [69927, "SRR19182980", "SRX15248096", "SRS12980679", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "CTRL 3", null, "strain:not applicable|isolate:CTRL|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S976", "S976", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "CTRL_3_1.fq.gz CTRL_3_2.fq.gz", "fastq fastq", 7089997200.0, 23633324.0, "CTRL 3 1.fq.gz", "0:150 1:150", "A:1809068567;C:1747946796;G:1737178132;T:1795714892;N:88813", 150, 150, null, null, 1809068567, 1747946796, 1737178132, 1795714892, 88813, "SRX15248096", "SRS12980679", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.9703, 0.96996, 0.03512, 0.03537, 0.68091, 0.68138, 0.48622, 0.48543, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [69928, "SRR19182981", "SRX15248095", "SRS12980678", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "CTRL 2", null, "strain:not applicable|isolate:CTRL|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S975", "S975", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "CTRL_2_1.fq.gz CTRL_2_2.fq.gz", "fastq fastq", 6787337700.0, 22624459.0, "CTRL 2 1.fq.gz", "0:150 1:150", "A:1743130460;C:1661481841;G:1649865815;T:1732778180;N:81404", 150, 150, null, null, 1743130460, 1661481841, 1649865815, 1732778180, 81404, "SRX15248095", "SRS12980678", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.96887, 0.9547, 0.04062, 0.03969, 0.67367, 0.67501, 0.48621, 0.49601, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [69929, "SRR19182982", "SRX15248094", "SRS12980677", "SRP375042", "PRJNA837558", "Danio rerio Raw sequence reads", "PRJNA837558", "Whole Genome Sequencing", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "CTRL 1", null, "strain:not applicable|isolate:CTRL|breed:zebrafish|cultivar:not applicable|ecotype:AB line|age:6 dpf|sex:not determined|tissue:larvae|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio", "S974", "S974", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP375042", null, null, "CTRL_1_1.fq.gz CTRL_1_2.fq.gz", "fastq fastq", 7077739800.0, 23592466.0, "CTRL 1 1.fq.gz", "0:150 1:150", "A:1822919843;C:1728663803;G:1713810517;T:1812263801;N:81836", 150, 150, null, null, 1822919843, 1728663803, 1713810517, 1812263801, 81836, "SRX15248094", "SRS12980677", "SRA1419650", "Lanzhou University|School ofLife Sciences", "Lanzhou University", 2, 0.96787, 0.9681, 0.03814, 0.0381, 0.6761, 0.67527, 0.48259, 0.48488, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-13", "Larval", "Larval", "Undetermined", "Undetermined"], [71050, "SRR21177740", "SRX17188838", "SRS14757966", "SRP393518", "PRJNA871389", "Danio rerio Transcriptome or Gene expression", "PRJNA871389", "Other", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "M4", null, "strain:AB strain|isolate:medicine treated|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:14 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "S578", "S578", "normal RNA Seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393518", null, null, "M4_1.fq M4_2.fq", "fastq fastq", 6460140600.0, 21533802.0, "M4 1.fq", "0:150 1:150", "A:1744397242;C:1495136658;G:1496481256;T:1724062549;N:62895", 150, 150, null, null, 1744397242, 1495136658, 1496481256, 1724062549, 62895, "SRX17188838", "SRS14757966", "SRA1481756", "Zhejiang University of Technology|Biological Engineering", "Zhejiang University of Technology", 2, 0.94226, 0.94199, 0.1206, 0.12012, 0.69457, 0.69369, 0.4645, 0.46351, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-23", "Larval", "Larval", "Undetermined", "Undetermined"], [71051, "SRR21177741", "SRX17188837", "SRS14757965", "SRP393518", "PRJNA871389", "Danio rerio Transcriptome or Gene expression", "PRJNA871389", "Other", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "M3", null, "strain:AB strain|isolate:medicine treated|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:13 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "S577", "S577", "normal RNA Seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393518", null, null, "M3_1.fq M3_2.fq", "fastq fastq", 6762812700.0, 22542709.0, "M3 1.fq", "0:150 1:150", "A:1800507274;C:1591193580;G:1592059789;T:1778991859;N:60198", 150, 150, null, null, 1800507274, 1591193580, 1592059789, 1778991859, 60198, "SRX17188837", "SRS14757965", "SRA1481756", "Zhejiang University of Technology|Biological Engineering", "Zhejiang University of Technology", 2, 0.94332, 0.94689, 0.0979, 0.09651, 0.70354, 0.70295, 0.45954, 0.46322, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-23", "Larval", "Larval", "Undetermined", "Undetermined"], [71052, "SRR21177742", "SRX17188836", "SRS14757964", "SRP393518", "PRJNA871389", "Danio rerio Transcriptome or Gene expression", "PRJNA871389", "Other", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "M2", null, "strain:AB strain|isolate:medicine treated|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:12 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "S576", "S576", "normal RNA Seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393518", null, null, "M2_1.fq M2_2.fq", "fastq fastq", 7208993100.0, 24029977.0, "M2 1.fq", "0:150 1:150", "A:1938011083;C:1676510621;G:1680553055;T:1913896553;N:21788", 150, 150, null, null, 1938011083, 1676510621, 1680553055, 1913896553, 21788, "SRX17188836", "SRS14757964", "SRA1481756", "Zhejiang University of Technology|Biological Engineering", "Zhejiang University of Technology", 2, 0.94477, 0.94444, 0.11271, 0.11255, 0.69469, 0.69475, 0.45826, 0.45744, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-23", "Larval", "Larval", "Undetermined", "Undetermined"], [71053, "SRR21177743", "SRX17188835", "SRS14757963", "SRP393518", "PRJNA871389", "Danio rerio Transcriptome or Gene expression", "PRJNA871389", "Other", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "M1", null, "strain:AB strain|isolate:medicine treated|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:11 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "S575", "S575", "normal RNA Seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393518", null, null, "M1_1.fq M1_2.fq", "fastq fastq", 6093560400.0, 20311868.0, "M1 1.fq", "0:150 1:150", "A:1638157819;C:1419235608;G:1415986411;T:1620147777;N:32785", 150, 150, null, null, 1638157819, 1419235608, 1415986411, 1620147777, 32785, "SRX17188835", "SRS14757963", "SRA1481756", "Zhejiang University of Technology|Biological Engineering", "Zhejiang University of Technology", 2, 0.94429, 0.94391, 0.11763, 0.11645, 0.69094, 0.69104, 0.46894, 0.46929, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-23", "Larval", "Larval", "Undetermined", "Undetermined"], [71054, "SRR21177744", "SRX17188834", "SRS14757962", "SRP393518", "PRJNA871389", "Danio rerio Transcriptome or Gene expression", "PRJNA871389", "Other", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "CONQ4", null, "strain:AB strain|isolate:abnormal|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:10 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "S574", "S574", "normal RNA Seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393518", null, null, "CONQ4_1.fq CONQ4_2.fq", "fastq fastq", 6203678700.0, 20678929.0, "CONQ4 1.fq", "0:150 1:150", "A:1636904617;C:1471084558;G:1472453592;T:1623176302;N:59631", 150, 150, null, null, 1636904617, 1471084558, 1472453592, 1623176302, 59631, "SRX17188834", "SRS14757962", "SRA1481756", "Zhejiang University of Technology|Biological Engineering", "Zhejiang University of Technology", 2, 0.94962, 0.94894, 0.09232, 0.09236, 0.67913, 0.67913, 0.46935, 0.46673, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-23", "Larval", "Larval", "Undetermined", "Undetermined"], [71055, "SRR21177745", "SRX17188833", "SRS14757961", "SRP393518", "PRJNA871389", "Danio rerio Transcriptome or Gene expression", "PRJNA871389", "Other", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "CONQ3", null, "strain:AB strain|isolate:abnormal|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:9 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "S573", "S573", "normal RNA Seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393518", null, null, "CONQ3_1.fq CONQ3_2.fq", "fastq fastq", 6743945100.0, 22479817.0, "CONQ3 1.fq", "0:150 1:150", "A:1775414763;C:1604473608;G:1604910553;T:1759101737;N:44439", 150, 150, null, null, 1775414763, 1604473608, 1604910553, 1759101737, 44439, "SRX17188833", "SRS14757961", "SRA1481756", "Zhejiang University of Technology|Biological Engineering", "Zhejiang University of Technology", 2, 0.95006, 0.94952, 0.08856, 0.08841, 0.68339, 0.68422, 0.46526, 0.46762, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-23", "Larval", "Larval", "Undetermined", "Undetermined"], [71056, "SRR21177746", "SRX17188832", "SRS14757960", "SRP393518", "PRJNA871389", "Danio rerio Transcriptome or Gene expression", "PRJNA871389", "Other", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "CONQ2", null, "strain:AB strain|isolate:abnormal|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:8 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "S572", "S572", "normal RNA Seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393518", null, null, "CONQ2_1.fq CONQ2_2.fq", "fastq fastq", 6766055100.0, 22553517.0, "CONQ2 1.fq", "0:150 1:150", "A:1779951961;C:1609850852;G:1608929111;T:1767259460;N:63716", 150, 150, null, null, 1779951961, 1609850852, 1608929111, 1767259460, 63716, "SRX17188832", "SRS14757960", "SRA1481756", "Zhejiang University of Technology|Biological Engineering", "Zhejiang University of Technology", 2, 0.95013, 0.95047, 0.08651, 0.08674, 0.68085, 0.68061, 0.45398, 0.46839, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-23", "Larval", "Larval", "Undetermined", "Undetermined"], [71057, "SRR21177747", "SRX17188831", "SRS14757959", "SRP393518", "PRJNA871389", "Danio rerio Transcriptome or Gene expression", "PRJNA871389", "Other", "normal transcriptome sequencing of Danio rerio", null, null, null, null, "CONQ1", null, "strain:AB strain|isolate:abnormal|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:7 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "S571", "S571", "normal RNA Seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393518", null, null, "CONQ1_1.fq CONQ1_2.fq", "fastq fastq", 6816197700.0, 22720659.0, "CONQ1 1.fq", "0:150 1:150", "A:1789803137;C:1624364787;G:1626102732;T:1775906053;N:20991", 150, 150, null, null, 1789803137, 1624364787, 1626102732, 1775906053, 20991, "SRX17188831", "SRS14757959", "SRA1481756", "Zhejiang University of Technology|Biological Engineering", "Zhejiang University of Technology", 2, 0.95146, 0.95073, 0.08742, 0.08638, 0.68034, 0.68071, 0.45545, 0.45201, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-23", "Larval", "Larval", "Undetermined", "Undetermined"], [76587, "SRR25204253", "SRX20951228", "SRS18227788", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "500+M 3", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "500+M 3", "500+M 3", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101380--D500+M_3.R1.raw.fastq.gz L1EGH3101380--D500+M_3.R2.raw.fastq.gz", "fastq fastq", 8511170266.0, 28182683.0, "L1EGH3101380  D500+M 3.R1.raw.fastq.gz", "0:151 1:151", "A:2227697379;C:2032526244;G:2114078273;T:2136804263;N:64107", 151, 151, null, null, 2227697379, 2032526244, 2114078273, 2136804263, 64107, "SRX20951228", "SRS18227788", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.95586, 0.95617, 0.03987, 0.03985, 0.6775, 0.68103, 0.49673, 0.49123, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"], [76588, "SRR25204254", "SRX20951227", "SRS18227789", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "500+M 2", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "500+M 2", "500+M 2", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101379--D500+M_2.R1.raw.fastq.gz L1EGH3101379--D500+M_2.R2.raw.fastq.gz", "fastq fastq", 6959039152.0, 23043176.0, "L1EGH3101379  D500+M 2.R1.raw.fastq.gz", "0:151 1:151", "A:1826205611;C:1651512663;G:1729908592;T:1751362435;N:49851", 151, 151, null, null, 1826205611, 1651512663, 1729908592, 1751362435, 49851, "SRX20951227", "SRS18227789", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.95499, 0.95399, 0.04627, 0.04671, 0.65945, 0.66383, 0.48455, 0.47538, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"], [76589, "SRR25204255", "SRX20951226", "SRS18227787", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "500+M 1", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "500+M 1", "500+M 1", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101378--D500+M_1.R1.raw.fastq.gz L1EGH3101378--D500+M_1.R2.raw.fastq.gz", "fastq fastq", 7797624900.0, 25819950.0, "L1EGH3101378  D500+M 1.R1.raw.fastq.gz", "0:151 1:151", "A:2029965653;C:1871228929;G:1936430185;T:1959940726;N:59407", 151, 151, null, null, 2029965653, 1871228929, 1936430185, 1959940726, 59407, "SRX20951226", "SRS18227787", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.9544, 0.95473, 0.04181, 0.04157, 0.66474, 0.66622, 0.48554, 0.47543, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"], [76590, "SRR25204256", "SRX20951225", "SRS18227786", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "500 3", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "500 3", "500 3", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101377--D500_3.R1.raw.fastq.gz L1EGH3101377--D500_3.R2.raw.fastq.gz", "fastq fastq", 7755527308.0, 25680554.0, "L1EGH3101377  D500 3.R1.raw.fastq.gz", "0:151 1:151", "A:2014113043;C:1865787204;G:1931889271;T:1943679942;N:57848", 151, 151, null, null, 2014113043, 1865787204, 1931889271, 1943679942, 57848, "SRX20951225", "SRS18227786", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.95529, 0.95554, 0.03686, 0.03684, 0.66939, 0.67198, 0.48406, 0.48577, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"], [76591, "SRR25204257", "SRX20951224", "SRS18227784", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "500 2", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "500 2", "500 2", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101376--D500_2.R1.raw.fastq.gz L1EGH3101376--D500_2.R2.raw.fastq.gz", "fastq fastq", 8164779588.0, 27035694.0, "L1EGH3101376  D500 2.R1.raw.fastq.gz", "0:151 1:151", "A:2145721904;C:1938384185;G:2018262699;T:2062351129;N:59671", 151, 151, null, null, 2145721904, 1938384185, 2018262699, 2062351129, 59671, "SRX20951224", "SRS18227784", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.95108, 0.95206, 0.04995, 0.04967, 0.65695, 0.65967, 0.4773, 0.47401, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"], [76592, "SRR25204258", "SRX20951223", "SRS18227785", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "500 1", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "500 1", "500 1", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101375--D500_1.R1.raw.fastq.gz L1EGH3101375--D500_1.R2.raw.fastq.gz", "fastq fastq", 7124410728.0, 23590764.0, "L1EGH3101375  D500 1.R1.raw.fastq.gz", "0:151 1:151", "A:1878629209;C:1682144847;G:1758829885;T:1804752117;N:54670", 151, 151, null, null, 1878629209, 1682144847, 1758829885, 1804752117, 54670, "SRX20951223", "SRS18227785", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.95332, 0.95346, 0.0512, 0.05133, 0.65583, 0.658, 0.48226, 0.48286, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"], [76593, "SRR25204259", "SRX20951222", "SRS18227783", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "Control 0 3", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "Control 0 3", "Control 0 3", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101374--D0_3.R1.raw.fastq.gz L1EGH3101374--D0_3.R2.raw.fastq.gz", "fastq fastq", 7096935674.0, 23499787.0, "L1EGH3101374  D0 3.R1.raw.fastq.gz", "0:151 1:151", "A:1876239823;C:1661281561;G:1757033088;T:1802327080;N:54122", 151, 151, null, null, 1876239823, 1661281561, 1757033088, 1802327080, 54122, "SRX20951222", "SRS18227783", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.95208, 0.9523, 0.05571, 0.05498, 0.65271, 0.65563, 0.48123, 0.48933, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"], [76594, "SRR25204260", "SRX20951221", "SRS18227782", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "Control 0 2", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "Control 0 2", "Control 0 2", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101373--D0_2.R1.raw.fastq.gz L1EGH3101373--D0_2.R2.raw.fastq.gz", "fastq fastq", 6917165946.0, 22904523.0, "L1EGH3101373  D0 2.R1.raw.fastq.gz", "0:151 1:151", "A:1809570420;C:1639682770;G:1725383993;T:1742476809;N:51954", 151, 151, null, null, 1809570420, 1639682770, 1725383993, 1742476809, 51954, "SRX20951221", "SRS18227782", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.95118, 0.95227, 0.04838, 0.04803, 0.66085, 0.66468, 0.48899, 0.47972, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"], [76595, "SRR25204261", "SRX20951220", "SRS18227781", "SRP448120", "PRJNA992237", "Danio rerio Raw sequence reads", "PRJNA992237", "Whole Genome Sequencing", "normal transcriptome of Danio rerio", null, null, null, null, "Control 0 1", null, "strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of Zebrafish Larvae", "Control 0 1", "Control 0 1", "Normal Transcriptome of Zebrafish Larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP448120", null, null, "L1EGH3101372--D0_1.R1.raw.fastq.gz L1EGH3101372--D0_1.R2.raw.fastq.gz", "fastq fastq", 7861598164.0, 26031782.0, "L1EGH3101372  D0 1.R1.raw.fastq.gz", "0:151 1:151", "A:2051039079;C:1878920378;G:1955076309;T:1976502641;N:59757", 151, 151, null, null, 2051039079, 1878920378, 1955076309, 1976502641, 59757, "SRX20951220", "SRS18227781", "SRA1669538", "Northwest A&amp;F University|College of Animal Science and Technology", "Northwest A&F University", 2, 0.95559, 0.95537, 0.04277, 0.04264, 0.66608, 0.6675, 0.48208, 0.47801, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-08", "Larval", "Larval", "Undetermined", "Undetermined"]], "truncated": false, "filtered_table_rows_count": 93, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "PAIRED", "p1": "Oligo-dT", "p2": "Undetermined"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 93, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 93, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "Oligo-dT", "label": "Oligo-dT", "count": 93, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&tissue_curation=Undetermined", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 93, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 71, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&experiment.platform=BGISEQ", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "Larval", "label": "Larval", "count": 76, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&devstage_curation_coarse=Larval", "selected": false}, {"value": "Adult", "label": "Adult", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&devstage_curation_coarse=Adult", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "Larval", "label": "Larval", "count": 76, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&devstage_curation=Larval", "selected": false}, {"value": "Adult", "label": "Adult", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&devstage_curation=Adult", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 93, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&tissue_curation_coarse=Undetermined", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 93, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined", "results": [{"value": "unknown", "label": "unknown", "count": 93, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=Oligo-dT&tissue_curation=Undetermined&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 78.12907599873142}