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123 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Undetermined"

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experiment.platform 3

devstage_curation_coarse 3

devstage_curation 3

experiment.library_layout 2

tissue_curation_coarse 1

  • Undetermined · 123 ✖

tissue_curation 1

technology 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 123 ✖

experiment.library_selection 1

  • Oligo-dT · 123 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
312 312 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 – non diabetic – 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…       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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
313 313 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 – non diabetic – 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…       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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
314 314 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 – non diabetic – 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…       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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
315 315 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 06 10 2016 15:53:35:325 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
316 316 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
317 317 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
318 318 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
319 319 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
320 320 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
322 322 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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 Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:33                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
323 323 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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 Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:32                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
324 324 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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 Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:31                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
325 325 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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 Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:30                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
326 326 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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 Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:29                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
327 327 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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 Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:28                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
328 328 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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 Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:27                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
329 329 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 ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   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 Tarifeño 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                 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   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   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     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   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
9918 9918 ERR5059480 ERX4865549 ERS5523939 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     aAM 6h rep1 JD AD30 PRPN1970901   ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AD30_PRPN197090.tar.gz nanopore 3739882337.0 3148027.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 0:1188.01 A:1054501690;C:834193435;G:847423060;T:1003764152;N:0 1188       1054501690 834193435 847423060 1003764152 0 ERX4865549 ERS5523939 ERA3206712 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9920 9920 ERR4330695 ERX4277529 ERS4811113 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 2h rep1 WT 2h rep1 SAMEA7050483 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-B2_PDBN005727.tar.gz fastq     ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1                       ERX4277529   ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9921 9921 ERR4327134 ERX4273968 ERS4808634 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep2 WT 4h rep2 SAMEA7048000 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AM39_PDBN042841.tar.gz nanopore 719646261.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 0:801.59 A:210217908;C:152963718;G:157393834;T:199070801;N:0 801       210217908 152963718 157393834 199070801 0 ERX4273968 ERS4808634 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9922 9922 ERR4330696 ERX4277530 ERS4811114 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep1 WT 4h rep1 JD C3 PDBN006177   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-C3_PDBN006177.tar.gz nanopore 4240799932.0 4331689.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 0:979.02 A:1229803846;C:914476674;G:943703560;T:1152815852;N:0 979       1229803846 914476674 943703560 1152815852 0 ERX4277530 ERS4811114 ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9923 9923 ERR4327135 ERX4273969 ERS4808635 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep1 WT 6h rep1 JD AC29 PDBN024889   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AC29_PDBN024889.tar.gz nanopore 1900324756.0 2013035.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 0:944.01 A:549431032;C:411510218;G:422103800;T:517279706;N:0 944       549431032 411510218 422103800 517279706 0 ERX4273969 ERS4808635 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9924 9924 ERR4326350 ERX4273208 ERS4808398 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   430 LNA 6h rep1 430 LNA 6h rep1 SAMEA7047764 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-H8_PDBN059569.tar.gz nanopore 722817654.0 657296.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 0:1099.68 A:206996491;C:157022109;G:155085437;T:203713617;N:0 1099       206996491 157022109 155085437 203713617 0 ERX4273208 ERS4808398 ERA2764399 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9925 9925 ERR4335436 ERX4282181 ERS4818366 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep2 WT 6h rep2 JD W23 PRPN039928   ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-W23_PRPN039928.tar.gz nanopore 1268761319.0 1385621.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1 0:915.66 A:366823862;C:275507684;G:284634548;T:341795225;N:0 915       366823862 275507684 284634548 341795225 0 ERX4282181 ERS4818366 ERA2769006 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9926 9926 ERR4321680 ERX4268538 ERS4808125 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 0h rep1 WT 0h rep1 JD A1 GDDN003032   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 GridION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE GridION   ERP122761 GridION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-A1_GDDN003032.tar.gz nanopore 753417826.0 698774.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 0:1078.20 A:214525685;C:165042952;G:171160615;T:202688574;N:0 1078       214525685 165042952 171160615 202688574 0 ERX4268538 ERS4808125 ERA2763718 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9951 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   RNA seq data of 5dpf larvae uninjected controls from the same batch. Uninjected2 Uninjected2   ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14         ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8                       ERX5601614   ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                             illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9952 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9953 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9954 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9955 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9956 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9957 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9958 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9959 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9960 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9961 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   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                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9962 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   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                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9963 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   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                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9964 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   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                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9965 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   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                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9966 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   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                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9967 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   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                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9968 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   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                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
9969 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   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                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:138 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   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     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   United States 2020-10-31 Larval Larval Undetermined Undetermined
31825 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.         PN 2   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1722127999 1463645587 1483173818 1716100796 0 SRX24268115 SRS21034395     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31826 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.         PN 1   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1827107021 1513034624 1533077624 1819674831 0 SRX24268114 SRS21034397     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31827 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.         EC 4   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1820989545 1516814697 1537970654 1813082104 0 SRX24268113 SRS21034396     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31828 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.         EC 3   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1821249100 1520587242 1541238550 1813478908 0 SRX24268112 SRS21034392     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31829 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.         EC 2   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1816692261 1527379142 1547365810 1810742187 0 SRX24268111 SRS21034391     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31830 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.         EC 1   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1812022780 1524359858 1544847441 1804823421 0 SRX24268110 SRS21034390     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31831 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.         Control 4   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1804178265 1523547469 1543839484 1798135282 0 SRX24268109 SRS21034388     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31832 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.         Control 3   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1808495506 1525725204 1545930043 1803368047 0 SRX24268108 SRS21034387     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31833 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.         PN 4   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1809816121 1508072480 1528272654 1803154845 0 SRX24268107 SRS21034386     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31834 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.         PN 3   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1802283686 1499008018 1519150002 1795672194 0 SRX24268106 SRS21034389     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31835 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.         Control 2   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1812352260 1531672703 1551377072 1806317165 0 SRX24268105 SRS21034385     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
31836 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.         Control 1   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP501894     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     1814883015 1537948710 1559376116 1808006659 0 SRX24268104 SRS21034384     Xiangyang No.1 People's Hospital, Hubei University of Medicine                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-04-15 Larval Larval Undetermined Undetermined
33350 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.     14   01H2   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                 RNA seq of daniorerio 01H2 01H2 Illumina NovaSeq 6000     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524293     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     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   China 2024-08-05 Larval Larval Undetermined Undetermined
35808 35808 SRR33047377 SRX28312718 SRS24651720 SRP577472 PRJNA1248424 Danio rerio Raw sequence reads PRJNA1248424 Whole Genome Sequencing The RNA seq of Danio rerio         WT4   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                 RNA seq of zebrafish WT4 WT4 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP577472     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     1937795555 1519113776 1563704738 1909641871 3401060 SRX28312718 SRS24651720 SRA2108999 Sun Yat-sen University|Sun Yat-sen University Sun Yat-sen University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-04-09 Larval Larval Undetermined Undetermined
35809 35809 SRR33047378 SRX28312717 SRS24651718 SRP577472 PRJNA1248424 Danio rerio Raw sequence reads PRJNA1248424 Whole Genome Sequencing The RNA seq of Danio rerio         WT3   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                 RNA seq of zebrafish WT3 WT3 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP577472     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     1955909582 1516895253 1552993746 1927330273 3641646 SRX28312717 SRS24651718 SRA2108999 Sun Yat-sen University|Sun Yat-sen University Sun Yat-sen University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-04-09 Larval Larval Undetermined Undetermined
35810 35810 SRR33047379 SRX28312716 SRS24651719 SRP577472 PRJNA1248424 Danio rerio Raw sequence reads PRJNA1248424 Whole Genome Sequencing The RNA seq of Danio rerio         WT2   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                 RNA seq of zebrafish WT2 WT2 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP577472     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     2101883253 1645411197 1682739575 2071755705 3675370 SRX28312716 SRS24651719 SRA2108999 Sun Yat-sen University|Sun Yat-sen University Sun Yat-sen University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-04-09 Larval Larval Undetermined Undetermined
35811 35811 SRR33047380 SRX28312715 SRS24651717 SRP577472 PRJNA1248424 Danio rerio Raw sequence reads PRJNA1248424 Whole Genome Sequencing The RNA seq of Danio rerio         WT1   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                 RNA seq of zebrafish WT1 WT1 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP577472     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     1920228684 1499116256 1529226612 1889060147 3582701 SRX28312715 SRS24651717 SRA2108999 Sun Yat-sen University|Sun Yat-sen University Sun Yat-sen University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-04-09 Larval Larval Undetermined Undetermined
35812 35812 SRR33047381 SRX28312714 SRS24651715 SRP577472 PRJNA1248424 Danio rerio Raw sequence reads PRJNA1248424 Whole Genome Sequencing The RNA seq of Danio rerio         ACE4   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                 RNA seq of zebrafish ACE4 ACE4 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP577472     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     1898072939 1518842682 1559008533 1871496075 2738071 SRX28312714 SRS24651715 SRA2108999 Sun Yat-sen University|Sun Yat-sen University Sun Yat-sen University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-04-09 Larval Larval Undetermined Undetermined
35813 35813 SRR33047382 SRX28312713 SRS24651714 SRP577472 PRJNA1248424 Danio rerio Raw sequence reads PRJNA1248424 Whole Genome Sequencing The RNA seq of Danio rerio         ACE3   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                 RNA seq of zebrafish ACE3 ACE3 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP577472     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     1810600301 1455285126 1501234399 1792186624 3408050 SRX28312713 SRS24651714 SRA2108999 Sun Yat-sen University|Sun Yat-sen University Sun Yat-sen University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-04-09 Larval Larval Undetermined Undetermined
35814 35814 SRR33047383 SRX28312712 SRS24651716 SRP577472 PRJNA1248424 Danio rerio Raw sequence reads PRJNA1248424 Whole Genome Sequencing The RNA seq of Danio rerio         ACE2   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                 RNA seq of zebrafish ACE2 ACE2 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP577472     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     1984084187 1557222983 1597912123 1960203230 3759677 SRX28312712 SRS24651716 SRA2108999 Sun Yat-sen University|Sun Yat-sen University Sun Yat-sen University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-04-09 Larval Larval Undetermined Undetermined
35815 35815 SRR33047384 SRX28312711 SRS24651712 SRP577472 PRJNA1248424 Danio rerio Raw sequence reads PRJNA1248424 Whole Genome Sequencing The RNA seq of Danio rerio         ACE1   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                 RNA seq of zebrafish ACE1 ACE1 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP577472     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     2020364086 1600073941 1649953306 1996832193 3925674 SRX28312711 SRS24651712 SRA2108999 Sun Yat-sen University|Sun Yat-sen University Sun Yat-sen University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-04-09 Larval Larval Undetermined Undetermined
55643 55643 SRR10604044 SRX7283593 SRS5777402 SRP235014 PRJNA594101 Danio rerio Transcriptome PRJNA594101 Other Danio rerio Transcriptome post cGAS and STING knockout         stko2   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                 RNA Seq of zebraish larvae sting knockout 2 sting knockout 2 RNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP235014     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     2864931942 2450585568 2436540783 2882828480 722527 SRX7283593 SRS5777402 SRA1007465 Shantou university medical college|Neuroscience Center Shantou university medical college 1 0.93079   0.07849   0.70301   0.47872   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2019-12-08 Larval Larval Undetermined Undetermined
55644 55644 SRR10604045 SRX7283592 SRS5777401 SRP235014 PRJNA594101 Danio rerio Transcriptome PRJNA594101 Other Danio rerio Transcriptome post cGAS and STING knockout         stko1   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                 RNA Seq of zebraish larvae sting knockout 1 sting knockout 1 RNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP235014     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     2823253748 2400078679 2379662427 2850274552 689594 SRX7283592 SRS5777401 SRA1007465 Shantou university medical college|Neuroscience Center Shantou university medical college 1 0.92736   0.08475   0.69822   0.47233   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2019-12-08 Larval Larval Undetermined Undetermined
55645 55645 SRR10604046 SRX7283591 SRS5777400 SRP235014 PRJNA594101 Danio rerio Transcriptome PRJNA594101 Other Danio rerio Transcriptome post cGAS and STING knockout         cgko2   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                 RNA Seq of zebraish larvae cgas knockout 2 cgas knockout 2 RNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP235014     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     2836737922 2388112649 2370425883 2866326601 633845 SRX7283591 SRS5777400 SRA1007465 Shantou university medical college|Neuroscience Center Shantou university medical college 1 0.93603   0.10606   0.67765   0.46153   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2019-12-08 Larval Larval Undetermined Undetermined
55646 55646 SRR10604047 SRX7283590 SRS5777399 SRP235014 PRJNA594101 Danio rerio Transcriptome PRJNA594101 Other Danio rerio Transcriptome post cGAS and STING knockout         cgko1   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                 RNA Seq of zebraish larvae cgas knockout 1 cgas knockout 1 RNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP235014     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     2845684832 2398817161 2379300746 2874108573 584188 SRX7283590 SRS5777399 SRA1007465 Shantou university medical college|Neuroscience Center Shantou university medical college 1 0.93684   0.10589   0.67933   0.48363   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2019-12-08 Larval Larval Undetermined Undetermined
55647 55647 SRR10604048 SRX7283589 SRS5777398 SRP235014 PRJNA594101 Danio rerio Transcriptome PRJNA594101 Other Danio rerio Transcriptome post cGAS and STING knockout         wt2   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                 RNA Seq of zebraish larvae wt normal 2 wt normal 2 RNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP235014     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     2906473511 2417423798 2405111864 2931146507 760720 SRX7283589 SRS5777398 SRA1007465 Shantou university medical college|Neuroscience Center Shantou university medical college 1 0.94167   0.11781   0.66831   0.4757   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2019-12-08 Larval Larval Undetermined Undetermined
55648 55648 SRR10604049 SRX7283588 SRS5777397 SRP235014 PRJNA594101 Danio rerio Transcriptome PRJNA594101 Other Danio rerio Transcriptome post cGAS and STING knockout         wt1   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                 RNA Seq of zebraish larvae wt nomal 1 wt nomal 1 RNA seq     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP235014     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     2896989124 2397285811 2382705623 2922067937 755505 SRX7283588 SRS5777397 SRA1007465 Shantou university medical college|Neuroscience Center Shantou university medical college 1 0.93947   0.11723   0.67203   0.45826   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2019-12-08 Larval Larval Undetermined Undetermined
66964 66964 SRR16965143 SRX13156592 SRS11088496 SRP346547 PRJNA780808 transcriptomics of carbendazim and enrofloxacin on zebrafish embryos PRJNA780808 Other reveal a interaction between ENF and CAR on metabolic regulation during development         1mix   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:10 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio :mixture group mix 1 mix 1 96hpf zebrafish larvae mixture group     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346547     mix2_1_2.fq.gz fastq 3313823250.0 22092155.0 mix2 1 2.fq.gz 0:0 1:150 A:895726357;C:763402657;G:745765587;T:908922686;N:5963 0 150     895726357 763402657 745765587 908922686 5963 SRX13156592 SRS11088496 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.93604   0.10794   0.65587   0.47956   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-17 Larval Larval Undetermined Undetermined
66965 66965 SRR16965144 SRX13156591 SRS11088495 SRP346547 PRJNA780808 transcriptomics of carbendazim and enrofloxacin on zebrafish embryos PRJNA780808 Other reveal a interaction between ENF and CAR on metabolic regulation during development         3enf   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:9 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio :enrofloxacin group enf 3 enf 3 96hpf zebrafish larvae enrofloxacin group     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346547     enf_3.fq.gz fastq 3304972350.0 22033149.0 enf 3.fq.gz 0:150 1:0 A:899427202;C:745999066;G:759917309;T:899625137;N:3636 150 0     899427202 745999066 759917309 899625137 3636 SRX13156591 SRS11088495 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.94353   0.10795   0.66212   0.47773   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-17 Larval Larval Undetermined Undetermined
66966 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         1enf   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                 RNA Seq of Danio rerio :enrofloxacin group enf 1 enf 1 96hpf zebrafish larvae enrofloxacin group     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP346547     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     1759651033 1563446116 1556912596 1772370048 9507 SRX13156590 SRS11088493 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.94992   0.06316   0.66979   0.48987   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-17 Larval Larval Undetermined Undetermined
66967 66967 SRR16965146 SRX13156589 SRS11088492 SRP346547 PRJNA780808 transcriptomics of carbendazim and enrofloxacin on zebrafish embryos PRJNA780808 Other reveal a interaction between ENF and CAR on metabolic regulation during development         3car   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio :carbendazim group car 3 car 3 96hpf zebrafish larvae carbendazim group     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346547     car_3_1.fq.gz fastq 3335622150.0 22237481.0 car 3 1.fq.gz 0:150 1:0 A:853229671;C:807433601;G:820478265;T:854475092;N:5521 150 0     853229671 807433601 820478265 854475092 5521 SRX13156589 SRS11088492 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.96567   0.03093   0.70997   0.47751   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-17 Larval Larval Undetermined Undetermined
66968 66968 SRR16965147 SRX13156588 SRS11088494 SRP346547 PRJNA780808 transcriptomics of carbendazim and enrofloxacin on zebrafish embryos PRJNA780808 Other reveal a interaction between ENF and CAR on metabolic regulation during development         1car   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:4 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio :carbendazim group car 1 car 1 96hpf zebrafish larvae carbendazim group     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346547     car_1_1.fq.gz fastq 3378056400.0 22520376.0 car 1 1.fq.gz 0:150 1:0 A:886009175;C:795203398;G:809447342;T:887390300;N:6185 150 0     886009175 795203398 809447342 887390300 6185 SRX13156588 SRS11088494 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.95701   0.05956   0.67836   0.4884   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-17 Larval Larval Undetermined Undetermined
66969 66969 SRR16965148 SRX13156587 SRS11088491 SRP346547 PRJNA780808 transcriptomics of carbendazim and enrofloxacin on zebrafish embryos PRJNA780808 Other reveal a interaction between ENF and CAR on metabolic regulation during development         3con   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio :control group con 3 con 3 96hpf zebrafish larvae control group     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346547     con_3_2.fq.gz fastq 3359054500.0 33590545.0 con 3 2.fq.gz 0:100 1:0 A:914533337;C:755914202;G:773676246;T:914930715;N:0 100 0     914533337 755914202 773676246 914930715 0 SRX13156587 SRS11088491 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.95076   0.10478   0.65646   0.49594   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-17 Larval Larval Undetermined Undetermined
66970 66970 SRR16965149 SRX13156586 SRS11088489 SRP346547 PRJNA780808 transcriptomics of carbendazim and enrofloxacin on zebrafish embryos PRJNA780808 Other reveal a interaction between ENF and CAR on metabolic regulation during development         3mix   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:12 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio :mixture group mix 3 mix 3 96hpf zebrafish larvae mixture group     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346547     mix2_3_1.fq.gz fastq 3362094000.0 33620940.0 mix2 3 1.fq.gz 0:100 1:0 A:916124379;C:755910593;G:768246534;T:921812494;N:0 100 0     916124379 755910593 768246534 921812494 0 SRX13156586 SRS11088489 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.94894   0.10416   0.65342   0.49475   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-17 Larval Larval Undetermined Undetermined
66971 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         2mix   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                 RNA Seq of Danio rerio :mixture group mix 2 mix 2 96hpf zebrafish larvae mixture group     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP346547     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     1815824677 1515086864 1506360115 1832433148 14296 SRX13156585 SRS11088490 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.93884   0.11657   0.65527   0.48114   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-17 Larval Larval Undetermined Undetermined
66972 66972 SRR16965151 SRX13156584 SRS11088488 SRP346547 PRJNA780808 transcriptomics of carbendazim and enrofloxacin on zebrafish embryos PRJNA780808 Other reveal a interaction between ENF and CAR on metabolic regulation during development         2con   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:2 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio :control group con 2 con 2 96hpf zebrafish larvae control group     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346547   loader:fastq load.py con_2_2.fq fastq 3324287550.0 22161917.0 con 2 2.fq.gz 0:150 A:848766265;C:812477645;G:798995610;T:864040426;N:7604 150       848766265 812477645 798995610 864040426 7604 SRX13156584 SRS11088488 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.95546   0.03524   0.70027   0.48649   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-22 Larval Larval Undetermined Undetermined
66973 66973 SRR16965152 SRX13156583 SRS11088487 SRP346547 PRJNA780808 transcriptomics of carbendazim and enrofloxacin on zebrafish embryos PRJNA780808 Other reveal a interaction between ENF and CAR on metabolic regulation during development         1con   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:1 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio :control group con 1 con 1 96hpf zebrafish larvae control group     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346547   loader:fastq load.py con_1_1.fq fastq 3330724500.0 22204830.0 con 1 1.fq.gz 0:150 A:896812508;C:762246067;G:774062043;T:897597946;N:5936 150       896812508 762246067 774062043 897597946 5936 SRX13156583 SRS11088487 SRA1329868 China Agricultural University|College of animal science and technology China Agricultural University 1 0.94926   0.08711   0.66789   0.48628   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-22 Larval Larval Undetermined Undetermined
66974 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.         1+mix   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP346418     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     1738687157 1575344731 1569683716 1755974708 9288 SRX13151074 SRS11083380 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.95161   0.05697   0.6817   0.48485   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66975 66975 SRR16959539 SRX13151073 SRS11083379 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.         2dim   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:8 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : dimethomorph group dim 2 dim 2 The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346418     dim_2_1.fq.gz fastq 3344257500.0 22295050.0 dim 2 1.fq.gz 0:150 1:0 A:895700119;C:767415749;G:784994320;T:896143585;N:3727 150 0     895700119 767415749 784994320 896143585 3727 SRX13151073 SRS11083379 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.9497   0.08418   0.66352   0.49341   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66976 66976 SRR16959540 SRX13151072 SRS11083378 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.         1dim   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:7 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : dimethomorph group dim 1 dim 1 The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346418     dim_1_1.fq.gz fastq 3318812250.0 22125415.0 dim 1 1.fq.gz 0:150 1:0 A:908481293;C:742787936;G:755930542;T:911608821;N:3658 150 0     908481293 742787936 755930542 911608821 3658 SRX13151072 SRS11083378 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.94211   0.11824   0.65344   0.47716   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66977 66977 SRR16959541 SRX13151071 SRS11083377 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.         3dif   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : difenoconazole group dif 3 dif 3 The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346418     dif_3_1.fq.gz fastq 3318453000.0 22123020.0 dif 3 1.fq.gz 0:150 1:0 A:893975607;C:758489621;G:772391705;T:893592335;N:3732 150 0     893975607 758489621 772391705 893592335 3732 SRX13151071 SRS11083377 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.94838   0.08393   0.66543   0.4818   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66978 66978 SRR16959542 SRX13151070 SRS11083376 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.         2dif   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:5 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : difenoconazole group dif 2 dif 2 The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346418     dif_2_2.fq.gz fastq 3304972350.0 22033149.0 dif 2 2.fq.gz 0:0 1:150 A:890456734;C:764917766;G:744757536;T:904833787;N:6527 0 150     890456734 764917766 744757536 904833787 6527 SRX13151070 SRS11083376 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.93514   0.107   0.6633   0.47599   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66979 66979 SRR16959543 SRX13151069 SRS11083375 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.         1dif   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:4 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : difenoconazole group dif 1 dif 1 The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346418     dif_1_1.fq.gz fastq 3295443900.0 21969626.0 dif 1 1.fq.gz 0:150 1:0 A:887936493;C:751636494;G:765508757;T:890358629;N:3527 150 0     887936493 751636494 765508757 890358629 3527 SRX13151069 SRS11083375 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.94623   0.09138   0.66478   0.4828   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66980 66980 SRR16959544 SRX13151068 SRS11083374 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.         3+con   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : control group con 3 con 3 The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346418     con_3_1.fq.gz fastq 3306406800.0 22042712.0 con 3 1.fq.gz 0:150 1:0 A:872740236;C:773482184;G:788334419;T:871846539;N:3422 150 0     872740236 773482184 788334419 871846539 3422 SRX13151068 SRS11083374 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.95458   0.06103   0.67409   0.48439   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66981 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.         2+mix   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                 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.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP346418     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     1782755416 1508342477 1501934674 1796820276 14057 SRX13151067 SRS11083373 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.93861   0.10685   0.66393   0.47194   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66982 66982 SRR16959546 SRX13151066 SRS11083372 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.         2+con   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:2 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : control group con 2 con 2 The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346418     con_2_2.fq.gz fastq 3324287550.0 22161917.0 con 2 2.fq.gz 0:0 1:150 A:848766265;C:812477645;G:798995610;T:864040426;N:7604 0 150     848766265 812477645 798995610 864040426 7604 SRX13151066 SRS11083372 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.95548   0.03524   0.70021   0.4867   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
66983 66983 SRR16959547 SRX13151065 SRS11083371 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.         1+con   strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:1 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : control group con 1 con 1 The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE BGISEQ BGISEQ-500   SRP346418     con_1_1.fq.gz fastq 3330724500.0 22204830.0 con 1 1.fq.gz 0:150 1:0 A:896812508;C:762246067;G:774062043;T:897597946;N:5936 150 0     896812508 762246067 774062043 897597946 5936 SRX13151065 SRS11083371 SRA1330365 China Agricultural University|College of animal science and technology China Agricultural University 1 0.94925   0.08711   0.66772   0.48635   150   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2021-11-16 Larval Larval Undetermined Undetermined
69921 69921 SRR19182974 SRX15248102 SRS12980685 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         Ni 100uM 3   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                 RNAseq of Danio rerio S982 S982 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined
69922 69922 SRR19182975 SRX15248101 SRS12980683 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         Ni 100uM 2   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                 RNAseq of Danio rerio S981 S981 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined
69923 69923 SRR19182976 SRX15248100 SRS12980682 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         Ni 100uM 1   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                 RNAseq of Danio rerio S980 S980 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined
69924 69924 SRR19182977 SRX15248099 SRS12980681 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         Ni 10uM 3   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                 RNAseq of Danio rerio S979 S979 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined
69925 69925 SRR19182978 SRX15248098 SRS12980680 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         Ni 10uM 2   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                 RNAseq of Danio rerio S978 S978 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined
69926 69926 SRR19182979 SRX15248097 SRS12980684 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         Ni 10uM 1   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                 RNAseq of Danio rerio S977 S977 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined
69927 69927 SRR19182980 SRX15248096 SRS12980679 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         CTRL 3   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                 RNAseq of Danio rerio S976 S976 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined
69928 69928 SRR19182981 SRX15248095 SRS12980678 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         CTRL 2   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                 RNAseq of Danio rerio S975 S975 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined
69929 69929 SRR19182982 SRX15248094 SRS12980677 SRP375042 PRJNA837558 Danio rerio Raw sequence reads PRJNA837558 Whole Genome Sequencing normal transcriptome sequencing of Danio rerio         CTRL 1   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                 RNAseq of Danio rerio S974 S974 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP375042     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     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   China 2022-05-13 Larval Larval Undetermined Undetermined

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