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77 rows where experiment.library_selection = "Oligo-dT", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Undetermined"

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experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Undetermined · 77 ✖

tissue_curation 1

technology 1

experiment.platform 1

  • ILLUMINA · 77 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 77 ✖
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
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
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
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
71050 71050 SRR21177740 SRX17188838 SRS14757966 SRP393518 PRJNA871389 Danio rerio Transcriptome or Gene expression PRJNA871389 Other normal transcriptome sequencing of Danio rerio         M4   strain:AB strain|isolate:medicine treated|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:14 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio S578 S578 normal RNA Seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP393518     M4_1.fq M4_2.fq fastq fastq 6460140600.0 21533802.0 M4 1.fq 0:150 1:150 A:1744397242;C:1495136658;G:1496481256;T:1724062549;N:62895 150 150     1744397242 1495136658 1496481256 1724062549 62895 SRX17188838 SRS14757966 SRA1481756 Zhejiang University of Technology|Biological Engineering Zhejiang University of Technology 2 0.94226 0.94199 0.1206 0.12012 0.69457 0.69369 0.4645 0.46351 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-08-23 Larval Larval Undetermined Undetermined
71051 71051 SRR21177741 SRX17188837 SRS14757965 SRP393518 PRJNA871389 Danio rerio Transcriptome or Gene expression PRJNA871389 Other normal transcriptome sequencing of Danio rerio         M3   strain:AB strain|isolate:medicine treated|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:13 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio S577 S577 normal RNA Seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP393518     M3_1.fq M3_2.fq fastq fastq 6762812700.0 22542709.0 M3 1.fq 0:150 1:150 A:1800507274;C:1591193580;G:1592059789;T:1778991859;N:60198 150 150     1800507274 1591193580 1592059789 1778991859 60198 SRX17188837 SRS14757965 SRA1481756 Zhejiang University of Technology|Biological Engineering Zhejiang University of Technology 2 0.94332 0.94689 0.0979 0.09651 0.70354 0.70295 0.45954 0.46322 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-08-23 Larval Larval Undetermined Undetermined
71052 71052 SRR21177742 SRX17188836 SRS14757964 SRP393518 PRJNA871389 Danio rerio Transcriptome or Gene expression PRJNA871389 Other normal transcriptome sequencing of Danio rerio         M2   strain:AB strain|isolate:medicine treated|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:12 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio S576 S576 normal RNA Seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP393518     M2_1.fq M2_2.fq fastq fastq 7208993100.0 24029977.0 M2 1.fq 0:150 1:150 A:1938011083;C:1676510621;G:1680553055;T:1913896553;N:21788 150 150     1938011083 1676510621 1680553055 1913896553 21788 SRX17188836 SRS14757964 SRA1481756 Zhejiang University of Technology|Biological Engineering Zhejiang University of Technology 2 0.94477 0.94444 0.11271 0.11255 0.69469 0.69475 0.45826 0.45744 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-08-23 Larval Larval Undetermined Undetermined
71053 71053 SRR21177743 SRX17188835 SRS14757963 SRP393518 PRJNA871389 Danio rerio Transcriptome or Gene expression PRJNA871389 Other normal transcriptome sequencing of Danio rerio         M1   strain:AB strain|isolate:medicine treated|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:11 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio S575 S575 normal RNA Seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP393518     M1_1.fq M1_2.fq fastq fastq 6093560400.0 20311868.0 M1 1.fq 0:150 1:150 A:1638157819;C:1419235608;G:1415986411;T:1620147777;N:32785 150 150     1638157819 1419235608 1415986411 1620147777 32785 SRX17188835 SRS14757963 SRA1481756 Zhejiang University of Technology|Biological Engineering Zhejiang University of Technology 2 0.94429 0.94391 0.11763 0.11645 0.69094 0.69104 0.46894 0.46929 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-08-23 Larval Larval Undetermined Undetermined
71054 71054 SRR21177744 SRX17188834 SRS14757962 SRP393518 PRJNA871389 Danio rerio Transcriptome or Gene expression PRJNA871389 Other normal transcriptome sequencing of Danio rerio         CONQ4   strain:AB strain|isolate:abnormal|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:10 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio S574 S574 normal RNA Seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP393518     CONQ4_1.fq CONQ4_2.fq fastq fastq 6203678700.0 20678929.0 CONQ4 1.fq 0:150 1:150 A:1636904617;C:1471084558;G:1472453592;T:1623176302;N:59631 150 150     1636904617 1471084558 1472453592 1623176302 59631 SRX17188834 SRS14757962 SRA1481756 Zhejiang University of Technology|Biological Engineering Zhejiang University of Technology 2 0.94962 0.94894 0.09232 0.09236 0.67913 0.67913 0.46935 0.46673 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-08-23 Larval Larval Undetermined Undetermined
71055 71055 SRR21177745 SRX17188833 SRS14757961 SRP393518 PRJNA871389 Danio rerio Transcriptome or Gene expression PRJNA871389 Other normal transcriptome sequencing of Danio rerio         CONQ3   strain:AB strain|isolate:abnormal|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:9 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio S573 S573 normal RNA Seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP393518     CONQ3_1.fq CONQ3_2.fq fastq fastq 6743945100.0 22479817.0 CONQ3 1.fq 0:150 1:150 A:1775414763;C:1604473608;G:1604910553;T:1759101737;N:44439 150 150     1775414763 1604473608 1604910553 1759101737 44439 SRX17188833 SRS14757961 SRA1481756 Zhejiang University of Technology|Biological Engineering Zhejiang University of Technology 2 0.95006 0.94952 0.08856 0.08841 0.68339 0.68422 0.46526 0.46762 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-08-23 Larval Larval Undetermined Undetermined
71056 71056 SRR21177746 SRX17188832 SRS14757960 SRP393518 PRJNA871389 Danio rerio Transcriptome or Gene expression PRJNA871389 Other normal transcriptome sequencing of Danio rerio         CONQ2   strain:AB strain|isolate:abnormal|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:8 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio S572 S572 normal RNA Seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP393518     CONQ2_1.fq CONQ2_2.fq fastq fastq 6766055100.0 22553517.0 CONQ2 1.fq 0:150 1:150 A:1779951961;C:1609850852;G:1608929111;T:1767259460;N:63716 150 150     1779951961 1609850852 1608929111 1767259460 63716 SRX17188832 SRS14757960 SRA1481756 Zhejiang University of Technology|Biological Engineering Zhejiang University of Technology 2 0.95013 0.95047 0.08651 0.08674 0.68085 0.68061 0.45398 0.46839 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-08-23 Larval Larval Undetermined Undetermined
71057 71057 SRR21177747 SRX17188831 SRS14757959 SRP393518 PRJNA871389 Danio rerio Transcriptome or Gene expression PRJNA871389 Other normal transcriptome sequencing of Danio rerio         CONQ1   strain:AB strain|isolate:abnormal|breed:not applicable|cultivar:not applicable|ecotype:not collected|age:7 days|dev stage:larvae|sex:not determined|tissue:total RNA|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio S571 S571 normal RNA Seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP393518     CONQ1_1.fq CONQ1_2.fq fastq fastq 6816197700.0 22720659.0 CONQ1 1.fq 0:150 1:150 A:1789803137;C:1624364787;G:1626102732;T:1775906053;N:20991 150 150     1789803137 1624364787 1626102732 1775906053 20991 SRX17188831 SRS14757959 SRA1481756 Zhejiang University of Technology|Biological Engineering Zhejiang University of Technology 2 0.95146 0.95073 0.08742 0.08638 0.68034 0.68071 0.45545 0.45201 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-08-23 Larval Larval Undetermined Undetermined
71591 71591 SRR21773952 SRX17768899 SRS15295762 SRP400510 PRJNA885753 Danio rerio Raw sequence reads PRJNA885753 Whole Genome Sequencing normal Transcriptome sequencing of zebrafish         ISL 3   strain:AB|breed:fish|age:96 hpf|sex:not applicable|tissue:larvae|replicate:replicate=biological replicate 6|BioSampleModel:Model organism or animal                 RNA seq of zrbrafish ISL 3 ISL 3 NORMAL RNA SEQ OF zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP400510     L1EFH311741--MJ_3.R1.raw.fastq.gz fastq 3636106123.0 24080173.0 L1EFH311741 MJ 3.R1.raw.fastq.gz 0:151 1:0 A:986029307;C:836470528;G:856224433;T:957306917;N:74938 151 0     986029307 836470528 856224433 957306917 74938 SRX17768899 SRS15295762 SRA1510923 Jiangxi Maternal and Child Health Hospital|Oncology Department Jiangxi Maternal and Child Health Hospital 1 0.95201   0.07421   0.72995   0.47689   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-10-01 Larval Larval Undetermined Undetermined
71592 71592 SRR21773953 SRX17768898 SRS15295761 SRP400510 PRJNA885753 Danio rerio Raw sequence reads PRJNA885753 Whole Genome Sequencing normal Transcriptome sequencing of zebrafish         ISL 2   strain:AB|breed:fish|age:96 hpf|sex:not applicable|tissue:larvae|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal                 RNA seq of zrbrafish ISL 2 ISL 2 NORMAL RNA SEQ OF zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP400510     L1EFH311740--MJ_2.R1.raw.fastq.gz fastq 4009114024.0 26550424.0 L1EFH311740 MJ 2.R1.raw.fastq.gz 0:151 1:0 A:1082365671;C:927178308;G:942280451;T:1057206324;N:83270 151 0     1082365671 927178308 942280451 1057206324 83270 SRX17768898 SRS15295761 SRA1510923 Jiangxi Maternal and Child Health Hospital|Oncology Department Jiangxi Maternal and Child Health Hospital 1 0.93235   0.11003   0.67403   0.46386   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-10-01 Larval Larval Undetermined Undetermined
71593 71593 SRR21773954 SRX17768897 SRS15295760 SRP400510 PRJNA885753 Danio rerio Raw sequence reads PRJNA885753 Whole Genome Sequencing normal Transcriptome sequencing of zebrafish         ISL 1   strain:AB|breed:fish|age:96 hpf|sex:not applicable|tissue:larvae|replicate:replicate=biological replicate 4|BioSampleModel:Model organism or animal                 RNA seq of zrbrafish ISL 1 ISL 1 NORMAL RNA SEQ OF zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP400510     L1EFH311739--MJ_1.R1.raw.fastq.gz fastq 3727259840.0 24683840.0 L1EFH311739 MJ 1.R1.raw.fastq.gz 0:151 1:0 A:1010831433;C:857231895;G:874029152;T:985090673;N:76687 151 0     1010831433 857231895 874029152 985090673 76687 SRX17768897 SRS15295760 SRA1510923 Jiangxi Maternal and Child Health Hospital|Oncology Department Jiangxi Maternal and Child Health Hospital 1 0.93354   0.11328   0.67142   0.46153   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-10-01 Larval Larval Undetermined Undetermined
71594 71594 SRR21773955 SRX17768896 SRS15295759 SRP400510 PRJNA885753 Danio rerio Raw sequence reads PRJNA885753 Whole Genome Sequencing normal Transcriptome sequencing of zebrafish         DMSO 3   strain:AB|breed:fish|age:96 hpf|sex:not applicable|tissue:larvae|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of zrbrafish DMSO 3 DMSO 3 NORMAL RNA SEQ OF zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP400510     L1EFH311744--MJC_3.R1.raw.fastq.gz fastq 3786330134.0 25075034.0 L1EFH311744 MJC 3.R1.raw.fastq.gz 0:151 1:0 A:1019293395;C:877604419;G:892262588;T:997091221;N:78511 151 0     1019293395 877604419 892262588 997091221 78511 SRX17768896 SRS15295759 SRA1510923 Jiangxi Maternal and Child Health Hospital|Oncology Department Jiangxi Maternal and Child Health Hospital 1 0.9339   0.10346   0.67243   0.46972   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-10-01 Larval Larval Undetermined Undetermined
71595 71595 SRR21773956 SRX17768895 SRS15295758 SRP400510 PRJNA885753 Danio rerio Raw sequence reads PRJNA885753 Whole Genome Sequencing normal Transcriptome sequencing of zebrafish         DMSO 2   strain:AB|breed:fish|age:96 hpf|sex:not applicable|tissue:larvae|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of zrbrafish DMSO 2 DMSO 2 NORMAL RNA SEQ OF zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP400510     L1EFH311743--MJC_2.R1.raw.fastq.gz fastq 3687067868.0 24417668.0 L1EFH311743 MJC 2.R1.raw.fastq.gz 0:151 1:0 A:984951883;C:863074103;G:876086315;T:962879156;N:76411 151 0     984951883 863074103 876086315 962879156 76411 SRX17768895 SRS15295758 SRA1510923 Jiangxi Maternal and Child Health Hospital|Oncology Department Jiangxi Maternal and Child Health Hospital 1 0.93417   0.10418   0.66949   0.46674   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-10-01 Larval Larval Undetermined Undetermined
71596 71596 SRR21773957 SRX17768894 SRS15295757 SRP400510 PRJNA885753 Danio rerio Raw sequence reads PRJNA885753 Whole Genome Sequencing normal Transcriptome sequencing of zebrafish         DMSO 1   strain:AB|breed:fish|age:96 hpf|sex:not applicable|tissue:larvae|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of zrbrafish DMSO 1 DMSO 1 NORMAL RNA SEQ OF zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP400510     L1EFH311742--MJC_1.R1.raw.fastq.gz fastq 3606182453.0 23882003.0 L1EFH311742 MJC 1.R1.raw.fastq.gz 0:151 1:0 A:958579858;C:844483137;G:861497670;T:941546853;N:74935 151 0     958579858 844483137 861497670 941546853 74935 SRX17768894 SRS15295757 SRA1510923 Jiangxi Maternal and Child Health Hospital|Oncology Department Jiangxi Maternal and Child Health Hospital 1 0.94042   0.08934   0.68396   0.47261   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-10-01 Larval Larval Undetermined Undetermined
76587 76587 SRR25204253 SRX20951228 SRS18227788 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         500+M 3   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae 500+M 3 500+M 3 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101380--D500+M_3.R1.raw.fastq.gz L1EGH3101380--D500+M_3.R2.raw.fastq.gz fastq fastq 8511170266.0 28182683.0 L1EGH3101380 D500+M 3.R1.raw.fastq.gz 0:151 1:151 A:2227697379;C:2032526244;G:2114078273;T:2136804263;N:64107 151 151     2227697379 2032526244 2114078273 2136804263 64107 SRX20951228 SRS18227788 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.95586 0.95617 0.03987 0.03985 0.6775 0.68103 0.49673 0.49123 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 Larval Larval Undetermined Undetermined
76588 76588 SRR25204254 SRX20951227 SRS18227789 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         500+M 2   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae 500+M 2 500+M 2 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101379--D500+M_2.R1.raw.fastq.gz L1EGH3101379--D500+M_2.R2.raw.fastq.gz fastq fastq 6959039152.0 23043176.0 L1EGH3101379 D500+M 2.R1.raw.fastq.gz 0:151 1:151 A:1826205611;C:1651512663;G:1729908592;T:1751362435;N:49851 151 151     1826205611 1651512663 1729908592 1751362435 49851 SRX20951227 SRS18227789 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.95499 0.95399 0.04627 0.04671 0.65945 0.66383 0.48455 0.47538 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 Larval Larval Undetermined Undetermined
76589 76589 SRR25204255 SRX20951226 SRS18227787 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         500+M 1   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae 500+M 1 500+M 1 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101378--D500+M_1.R1.raw.fastq.gz L1EGH3101378--D500+M_1.R2.raw.fastq.gz fastq fastq 7797624900.0 25819950.0 L1EGH3101378 D500+M 1.R1.raw.fastq.gz 0:151 1:151 A:2029965653;C:1871228929;G:1936430185;T:1959940726;N:59407 151 151     2029965653 1871228929 1936430185 1959940726 59407 SRX20951226 SRS18227787 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.9544 0.95473 0.04181 0.04157 0.66474 0.66622 0.48554 0.47543 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 Larval Larval Undetermined Undetermined
76590 76590 SRR25204256 SRX20951225 SRS18227786 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         500 3   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae 500 3 500 3 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101377--D500_3.R1.raw.fastq.gz L1EGH3101377--D500_3.R2.raw.fastq.gz fastq fastq 7755527308.0 25680554.0 L1EGH3101377 D500 3.R1.raw.fastq.gz 0:151 1:151 A:2014113043;C:1865787204;G:1931889271;T:1943679942;N:57848 151 151     2014113043 1865787204 1931889271 1943679942 57848 SRX20951225 SRS18227786 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.95529 0.95554 0.03686 0.03684 0.66939 0.67198 0.48406 0.48577 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 Larval Larval Undetermined Undetermined
76591 76591 SRR25204257 SRX20951224 SRS18227784 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         500 2   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae 500 2 500 2 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101376--D500_2.R1.raw.fastq.gz L1EGH3101376--D500_2.R2.raw.fastq.gz fastq fastq 8164779588.0 27035694.0 L1EGH3101376 D500 2.R1.raw.fastq.gz 0:151 1:151 A:2145721904;C:1938384185;G:2018262699;T:2062351129;N:59671 151 151     2145721904 1938384185 2018262699 2062351129 59671 SRX20951224 SRS18227784 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.95108 0.95206 0.04995 0.04967 0.65695 0.65967 0.4773 0.47401 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 Larval Larval Undetermined Undetermined
76592 76592 SRR25204258 SRX20951223 SRS18227785 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         500 1   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae 500 1 500 1 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101375--D500_1.R1.raw.fastq.gz L1EGH3101375--D500_1.R2.raw.fastq.gz fastq fastq 7124410728.0 23590764.0 L1EGH3101375 D500 1.R1.raw.fastq.gz 0:151 1:151 A:1878629209;C:1682144847;G:1758829885;T:1804752117;N:54670 151 151     1878629209 1682144847 1758829885 1804752117 54670 SRX20951223 SRS18227785 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.95332 0.95346 0.0512 0.05133 0.65583 0.658 0.48226 0.48286 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 Larval Larval Undetermined Undetermined
76593 76593 SRR25204259 SRX20951222 SRS18227783 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         Control 0 3   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae Control 0 3 Control 0 3 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101374--D0_3.R1.raw.fastq.gz L1EGH3101374--D0_3.R2.raw.fastq.gz fastq fastq 7096935674.0 23499787.0 L1EGH3101374 D0 3.R1.raw.fastq.gz 0:151 1:151 A:1876239823;C:1661281561;G:1757033088;T:1802327080;N:54122 151 151     1876239823 1661281561 1757033088 1802327080 54122 SRX20951222 SRS18227783 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.95208 0.9523 0.05571 0.05498 0.65271 0.65563 0.48123 0.48933 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 Larval Larval Undetermined Undetermined
76594 76594 SRR25204260 SRX20951221 SRS18227782 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         Control 0 2   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae Control 0 2 Control 0 2 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101373--D0_2.R1.raw.fastq.gz L1EGH3101373--D0_2.R2.raw.fastq.gz fastq fastq 6917165946.0 22904523.0 L1EGH3101373 D0 2.R1.raw.fastq.gz 0:151 1:151 A:1809570420;C:1639682770;G:1725383993;T:1742476809;N:51954 151 151     1809570420 1639682770 1725383993 1742476809 51954 SRX20951221 SRS18227782 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.95118 0.95227 0.04838 0.04803 0.66085 0.66468 0.48899 0.47972 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 Larval Larval Undetermined Undetermined
76595 76595 SRR25204261 SRX20951220 SRS18227781 SRP448120 PRJNA992237 Danio rerio Raw sequence reads PRJNA992237 Whole Genome Sequencing normal transcriptome of Danio rerio         Control 0 1   strain:AB|age:96 hpf|collection date:2021 12 20|geo loc name:not applicable|sex:not applicable|tissue:larvae|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 Transcriptome of Zebrafish Larvae Control 0 1 Control 0 1 Normal Transcriptome of Zebrafish Larvae     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP448120     L1EGH3101372--D0_1.R1.raw.fastq.gz L1EGH3101372--D0_1.R2.raw.fastq.gz fastq fastq 7861598164.0 26031782.0 L1EGH3101372 D0 1.R1.raw.fastq.gz 0:151 1:151 A:2051039079;C:1878920378;G:1955076309;T:1976502641;N:59757 151 151     2051039079 1878920378 1955076309 1976502641 59757 SRX20951220 SRS18227781 SRA1669538 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.95559 0.95537 0.04277 0.04264 0.66608 0.6675 0.48208 0.47801 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-07-08 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");;