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,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 progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,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,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 progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,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,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 progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
29719,SRR27485664,SRX23156885,SRS20107306,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,eggs R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: eggs  rep4,EV06009,EV06009,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06009.R1.fastq.gz,fastq,809138488.0,10734286.0,EV06009.R1.fastq.gz,0:75.38,A:236901398;C:156814193;G:179647937;T:235732894;N:42066,75,,,,236901398,156814193,179647937,235732894,42066,SRX23156885,SRS20107306,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.92159,,0.07516,,0.837,,0.7566,,69,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Undetermined,Embryo,Undetermined,Embryo Imprecise
29730,SRR27485675,SRX23156874,SRS20107295,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,eggs R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: eggs  rep4,EV06002,EV06002,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06002.R1.fastq.gz,fastq,632849068.0,8404028.0,EV06002.R1.fastq.gz,0:75.30,A:194183801;C:123105421;G:139266843;T:176255048;N:37955,75,,,,194183801,123105421,139266843,176255048,37955,SRX23156874,SRS20107295,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.88896,,0.09385,,0.81864,,0.73385,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Undetermined,Embryo,Undetermined,Embryo Imprecise
29737,SRR27477297,SRX23148650,SRS20099368,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,eggs R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: eggs  rep4,EV09002,EV09002,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09002.R1.fastq.gz,fastq,546999929.0,7270092.0,EV09002.R1.fastq.gz,0:75.24,A:165415993;C:110874896;G:124384517;T:146294099;N:30424,75,,,,165415993,110874896,124384517,146294099,30424,SRX23148650,SRS20099368,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.9065,,0.11883,,0.82231,,0.74466,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Undetermined,Embryo,Undetermined,Embryo Imprecise
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,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,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,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,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,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,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,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,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
60104,SRR12142045,SRX8663215,SRS6944340,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of lysate for FigS2,,zebrafish lysate biological replicate 4,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 4,Dre 4,cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g004_1.fastq.gz,fastq,509713380.0,9994380.0,DreSceMix g004 1.fastq.gz,0:51,A:251366594;C:61585710;G:62159129;T:134578953;N:22994,51,,,,251366594,61585710,62159129,134578953,22994,SRX8663215,SRS6944340,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.67392,,0.54102,,0.86476,,0.37091,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60105,SRR12141709,SRX8663075,SRS6944200,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of lysate for FigS2,,zebrafish lysate biological replicate 3,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 3,Dre 3,cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g003_1.fastq.gz,fastq,499717482.0,9798382.0,DreSceMix g003 1.fastq.gz,0:51,A:263221073;C:56114768;G:56547079;T:123812019;N:22543,51,,,,263221073,56114768,56547079,123812019,22543,SRX8663075,SRS6944200,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.63258,,0.48288,,0.86819,,0.35874,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60106,SRR12141808,SRX8662976,SRS6944101,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of purified RNA from lysate for Fig.S2,,zebrafish purifiedRNA biological replicate 6,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 12,Dre 12,cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g014_1.fastq.gz,fastq,421063599.0,8256149.0,DreSceMix g014 1.fastq.gz,0:51,A:207118237;C:53600213;G:54041718;T:106284709;N:18722,51,,,,207118237,53600213,54041718,106284709,18722,SRX8662976,SRS6944101,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.47999,,0.19308,,0.85977,,0.46733,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60107,SRR12141828,SRX8662956,SRS6944081,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of purified RNA from lysate for Fig.S2,,zebrafish purifiedRNA biological replicate 4,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 10,Dre 10,cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g012_1.fastq.gz,fastq,626464773.0,12283623.0,DreSceMix g012 1.fastq.gz,0:51,A:263307070;C:96744908;G:98635228;T:167749896;N:27671,51,,,,263307070,96744908,98635228,167749896,27671,SRX8662956,SRS6944081,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.50608,,0.14369,,0.83422,,0.45691,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60108,SRR12141839,SRX8662945,SRS6944070,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of purified RNA from lysate for Fig.S2,,zebrafish purifiedRNA biological replicate 3,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 9,Dre 9,cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g011_1.fastq.gz,fastq,436381296.0,8556496.0,DreSceMix g011 1.fastq.gz,0:51,A:205579619;C:58008903;G:59021026;T:113752218;N:19530,51,,,,205579619,58008903,59021026,113752218,19530,SRX8662945,SRS6944070,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.46615,,0.18281,,0.84778,,0.44592,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60109,SRR12141850,SRX8662934,SRS6944059,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of purified RNA from lysate for Fig.S2,,zebrafish purifiedRNA biological replicate 2,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 8,Dre 8,cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g010_1.fastq.gz,fastq,870727437.0,17073087.0,DreSceMix g010 1.fastq.gz,0:51,A:343772776;C:142428987;G:145570260;T:238917135;N:38279,51,,,,343772776,142428987,145570260,238917135,38279,SRX8662934,SRS6944059,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.52883,,0.1235,,0.82256,,0.45498,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60110,SRR12141861,SRX8662923,SRS6944047,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of purified RNA from lysate for Fig.S2,,zebrafish purifiedRNA biological replicate 1,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 7,Dre 7,cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g009_1.fastq.gz,fastq,1875928206.0,36782906.0,DreSceMix g009 1.fastq.gz,0:51,A:684015713;C:329272255;G:335557540;T:526999083;N:83615,51,,,,684015713,329272255,335557540,526999083,83615,SRX8662923,SRS6944047,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.58553,,0.11315,,0.8029,,0.4678,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60111,SRR12141872,SRX8662912,SRS6944037,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of lysate for FigS2,,zebrafish lysate biological replicate 6,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 6,Dre 6,cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g006_1.fastq.gz,fastq,390346044.0,7653844.0,DreSceMix g006 1.fastq.gz,0:51,A:194005234;C:46666192;G:46964771;T:102692143;N:17704,51,,,,194005234,46666192,46964771,102692143,17704,SRX8662912,SRS6944037,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.69496,,0.57077,,0.86864,,0.35451,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60112,SRR12141959,SRX8662825,SRS6943950,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of lysate for FigS2,,zebrafish lysate biological replicate 5,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 5,Dre 5,cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g005_1.fastq.gz,fastq,684050964.0,13412764.0,DreSceMix g005 1.fastq.gz,0:51,A:318875237;C:88359396;G:89394558;T:187391266;N:30507,51,,,,318875237,88359396,89394558,187391266,30507,SRX8662825,SRS6943950,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.61659,,0.4142,,0.8393,,0.42049,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60113,SRR12142001,SRX8662783,SRS6943908,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of purified RNA from lysate for Fig.S2,,zebrafish purifiedRNA biological replicate 5,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 11,Dre 11,cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g013_1.fastq.gz,fastq,998754318.0,19583418.0,DreSceMix g013 1.fastq.gz,0:51,A:402091762;C:156702863;G:160047354;T:279867921;N:44418,51,,,,402091762,156702863,160047354,279867921,44418,SRX8662783,SRS6943908,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.52766,,0.13651,,0.81237,,0.45557,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60114,SRR12142002,SRX8662782,SRS6943907,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of lysate for FigS2,,zebrafish lysate biological replicate 2,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 2,Dre 2,cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g002_1.fastq.gz,fastq,702610578.0,13776678.0,DreSceMix g002 1.fastq.gz,0:51,A:332485038;C:89482705;G:90437771;T:190173083;N:31981,51,,,,332485038,89482705,90437771,190173083,31981,SRX8662782,SRS6943907,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.63597,,0.45832,,0.85088,,0.40969,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
60115,SRR12142003,SRX8662781,SRS6943906,SRP269853,PRJNA643885,performance test of DeLTa Seq,PRJNA643885,Other,This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq,,,RNA Seq of lysate for FigS2,,zebrafish lysate biological replicate 1,,strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,DeLTa Seq,Dre 1,Dre 1,cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP269853,,,DreSceMix_g001_1.fastq.gz,fastq,1273185777.0,24964427.0,DreSceMix g001 1.fastq.gz,0:51,A:541573299;C:186989405;G:191401487;T:353163815;N:57771,51,,,,541573299,186989405,191401487,353163815,57771,SRX8662781,SRS6943906,SRA1094353,Ryukoku university|Fauculity of Agriculture,Ryukoku university,1,0.62046,,0.30937,,0.8197,,0.44014,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2020-07-03,Hatching,Embryo,Undetermined,Embryo Imprecise
69604,SRR18935955,SRX15013551,SRS12762156,SRP372447,PRJNA832566,zebrafish RBC sequencing,PRJNA832566,Other,profiling the distinct transcriptional identity of RBC from different RBC related mutants.,,,,,alad RBC,,strain:alad mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of RBC,L81332,L81332,FACS sorted alad mutant RBCs,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP372447,,,Alad-2_L7_I332.R1.clean.fastq.gz,fastq,3448675800.0,22991172.0,Alad 2 L7 I332.R1.clean.fastq.gz,0:150 1:0,A:909204217;C:819708757;G:815883274;T:903292138;N:587414,150,0,,,909204217,819708757,815883274,903292138,587414,SRX15013551,SRS12762156,SRA1410774,Chinese Acamedy of Sciences|Institute of zoology,Chinese Acamedy of Sciences,1,0.93973,,0.13997,,0.7685,,0.51168,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-04-27,Pharyngula,Embryo,Undetermined,Embryo Imprecise
69605,SRR18935956,SRX15013550,SRS12762156,SRP372447,PRJNA832566,zebrafish RBC sequencing,PRJNA832566,Other,profiling the distinct transcriptional identity of RBC from different RBC related mutants.,,,,,alad RBC,,strain:alad mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of RBC,L81331,L81331,FACS sorted alad mutant RBCs,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP372447,,,Alad-1_L8_I331.R1.clean.fastq.gz,fastq,3987610500.0,26584070.0,Alad 1 L8 I331.R1.clean.fastq.gz,0:150 1:0,A:1031398922;C:974521107;G:967367126;T:1013951504;N:371841,150,0,,,1031398922,974521107,967367126,1013951504,371841,SRX15013550,SRS12762156,SRA1410774,Chinese Acamedy of Sciences|Institute of zoology,Chinese Acamedy of Sciences,1,0.9447,,0.1019,,0.81286,,0.58316,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-04-27,Pharyngula,Embryo,Undetermined,Embryo Imprecise
69606,SRR18935957,SRX15013549,SRS12762155,SRP372447,PRJNA832566,zebrafish RBC sequencing,PRJNA832566,Other,profiling the distinct transcriptional identity of RBC from different RBC related mutants.,,,,,alas2 RBC,,strain:alas2 mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of RBC,L81330,L81330,FACS sorted alas2 mutant RBCs,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP372447,,,Alas2-2_L8_I330.R1.clean.fastq.gz,fastq,4163915100.0,27759434.0,Alas2 2 L8 I330.R1.clean.fastq.gz,0:150 1:0,A:1119245849;C:968636914;G:967111308;T:1108544148;N:376881,150,0,,,1119245849,968636914,967111308,1108544148,376881,SRX15013549,SRS12762155,SRA1410774,Chinese Acamedy of Sciences|Institute of zoology,Chinese Acamedy of Sciences,1,0.92608,,0.1778,,0.75471,,0.55161,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-04-27,Pharyngula,Embryo,Undetermined,Embryo Imprecise
69607,SRR18935958,SRX15013548,SRS12762155,SRP372447,PRJNA832566,zebrafish RBC sequencing,PRJNA832566,Other,profiling the distinct transcriptional identity of RBC from different RBC related mutants.,,,,,alas2 RBC,,strain:alas2 mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of RBC,L81329,L81329,FACS sorted alas2 mutant RBCs,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP372447,,,Alas2-1_L8_I329.R1.clean.fastq.gz,fastq,3953391150.0,26355941.0,Alas2 1 L8 I329.R1.clean.fastq.gz,0:150 1:0,A:1035309566;C:950958591;G:946245209;T:1020520823;N:356961,150,0,,,1035309566,950958591,946245209,1020520823,356961,SRX15013548,SRS12762155,SRA1410774,Chinese Acamedy of Sciences|Institute of zoology,Chinese Acamedy of Sciences,1,0.93024,,0.14212,,0.81213,,0.61442,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-04-27,Pharyngula,Embryo,Undetermined,Embryo Imprecise
69608,SRR18935959,SRX15013547,SRS12762154,SRP372447,PRJNA832566,zebrafish RBC sequencing,PRJNA832566,Other,profiling the distinct transcriptional identity of RBC from different RBC related mutants.,,,,,WT RBC,,strain:WT|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of RBC,L81328,L81328,FACS sorted WT RBCs,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP372447,,,WT-2_L8_I328.R1.clean.fastq.gz,fastq,3589015200.0,23926768.0,WT 2 L8 I328.R1.clean.fastq.gz,0:150 1:0,A:922300230;C:887849832;G:879590696;T:898942142;N:332300,150,0,,,922300230,887849832,879590696,898942142,332300,SRX15013547,SRS12762154,SRA1410774,Chinese Acamedy of Sciences|Institute of zoology,Chinese Acamedy of Sciences,1,0.94576,,0.09241,,0.83514,,0.68592,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-04-27,Pharyngula,Embryo,Undetermined,Embryo Imprecise
69609,SRR18935960,SRX15013546,SRS12762154,SRP372447,PRJNA832566,zebrafish RBC sequencing,PRJNA832566,Other,profiling the distinct transcriptional identity of RBC from different RBC related mutants.,,,,,WT RBC,,strain:WT|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of RBC,L81327,L81327,FACS sorted WT RBCs,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP372447,,,WT-1_L8_I327.R1.clean.fastq.gz,fastq,4062851700.0,27085678.0,WT 1 L8 I327.R1.clean.fastq.gz,0:150 1:0,A:1028410873;C:1020911876;G:1010215515;T:1002940085;N:373351,150,0,,,1028410873,1020911876,1010215515,1002940085,373351,SRX15013546,SRS12762154,SRA1410774,Chinese Acamedy of Sciences|Institute of zoology,Chinese Acamedy of Sciences,1,0.94919,,0.0692,,0.85567,,0.70156,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-04-27,Pharyngula,Embryo,Undetermined,Embryo Imprecise
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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