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
280,DRR161311,DRX151936,DRS095335,DRP005084,PRJDB7735,Gene expression profile in adult zebrafish liver,DRP005084,Transcriptome Analysis,Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.,,,,Transcriptome of female Danio rerio liver,SAMD00153247,,sample name:transcriptome zebrafish female|sex:female|strain:RIKEN WT|tissue:liver,,,,,,,,,NextSeq 500 paired end sequencing of SAMD00153247,DRX151936,f,1,1,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP005084,NextSeq 500 paired end sequencing of SAMD00153247,,,,2338564937.0,15498367.0,DRR161311,0:75.45 1:75.44,A:613899755;C:541756858;G:548366901;T:633083422;N:1458001,75,75,,,613899755,541756858,548366901,633083422,1458001,DRX151936,DRS095335,DRA007652,"OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine","Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine",2,0.95814,0.96362,0.05394,0.04517,0.77932,0.7834,0.37385,0.37264,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-05-20,Undetermined,Adult,Liver,Liver and Biliary System
281,DRR161310,DRX151935,DRS095334,DRP005084,PRJDB7735,Gene expression profile in adult zebrafish liver,DRP005084,Transcriptome Analysis,Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.,,,,Transcriptome of male Danio rerio liver,SAMD00153246,,sample name:transcriptome zebrafish male|sex:male|strain:RIKEN WT|tissue:liver,,,,,,,,,NextSeq 500 paired end sequencing of SAMD00153246,DRX151935,m,1,1,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP005084,NextSeq 500 paired end sequencing of SAMD00153246,,,,2506978527.0,16611154.0,DRR161310,0:75.48 1:75.44,A:672321355;C:568289588;G:569411670;T:695545626;N:1410288,75,75,,,672321355,568289588,569411670,695545626,1410288,DRX151935,DRS095334,DRA007652,"OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine","Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine",2,0.94746,0.95115,0.07899,0.06363,0.80837,0.8115,0.52008,0.58743,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-05-20,Undetermined,Adult,Liver,Liver and Biliary System
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
321,ERR977589,ERX1054572,ERS805778,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,,Beta cells from adults purified by FACS,Delta cells R3,SAMEA3498629,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498629|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:34|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:34,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 14,Delta 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-B176_SSTcells-03122013_CAGATC_L001_R1_001.fastq.gz NGS14-B176_SSTcells-03122013_CAGATC_L001_R2_001.fastq.gz,fastq fastq,17691597128.0,87582164.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 14,0:101 1:101,A:4843643109;C:3683816237;G:3736882877;T:5332210638;N:95044267,101,101,,,4843643109,3683816237,3736882877,5332210638,95044267,ERX1054572,ERS805778,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.92685,0.84146,0.10249,0.11723,0.76532,0.78309,0.39721,0.43714,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
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
330,ERR977580,ERX1054563,ERS805769,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,,Beta cells from adults purified by FACS,Beta cells R3,SAMEA3498620,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498620|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:25|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:25,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 5,Beta 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-B174_Betacells-03122013_GCCAAT_L002_R1_001.fastq.gz NGS14-B174_Betacells-03122013_GCCAAT_L002_R2_001.fastq.gz,fastq fastq,17625660086.0,87255743.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 5,0:101 1:101,A:4840276660;C:3724973884;G:3755195525;T:5214977933;N:90236084,101,101,,,4840276660,3724973884,3755195525,5214977933,90236084,ERX1054563,ERS805769,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90631,0.8718,0.11791,0.11942,0.76203,0.77638,0.53654,0.49457,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
331,ERR977579,ERX1054562,ERS805768,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,,Beta cells from adults purified by FACS,Beta cells R2 2,SAMEA3498619,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498619|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:24|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:24,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 4,Beta 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,BetaCell2_A026_ATGTCA_L004_R1_001.fastq.gz BetaCell2_A026_ATGTCA_L004_R2_001.fastq.gz,fastq fastq,8532015198.0,42237699.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 4,0:101 1:101,A:2314776471;C:1823939144;G:1839244845;T:2552984556;N:1070182,101,101,,,2314776471,1823939144,1839244845,2552984556,1070182,ERX1054562,ERS805768,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.69844,0.57999,0.09124,0.07501,0.80876,0.82964,0.56023,0.5159,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
332,ERR977578,ERX1054561,ERS805767,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,,Beta cells from adults purified by FACS,Beta cells R2 1,SAMEA3498618,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498618|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:23|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:23,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 3,Beta 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,BetaCell_ATGTCA_L005_R1_001.fastq.gz BetaCell_ATGTCA_L005_R2_001.fastq.gz,fastq fastq,3250611068.0,16092134.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 3,0:101 1:101,A:854826460;C:691024995;G:695294721;T:954934438;N:54530454,101,101,,,854826460,691024995,695294721,954934438,54530454,ERX1054561,ERS805767,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.67496,0.53873,0.08771,0.06606,0.80969,0.83433,0.56231,0.51717,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
333,ERR977577,ERX1054560,ERS805766,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,,Beta cells from adults purified by FACS,Beta cells R1 2,SAMEA3498617,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498617|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:22|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:22,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 2,Beta 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,BetaCell1_A003_GTCCGC_L004_R1_001.fastq.gz BetaCell1_A003_GTCCGC_L004_R2_001.fastq.gz,fastq fastq,3765102038.0,18639119.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 2,0:101 1:101,A:1050226787;C:789381360;G:801049952;T:1123973291;N:470648,101,101,,,1050226787,789381360,801049952,1123973291,470648,ERX1054560,ERS805766,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90456,0.86125,0.12934,0.13194,0.77721,0.79109,0.56708,0.53213,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
334,ERR977576,ERX1054559,ERS805765,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,,Beta cells from adults purified by FACS,Beta cells R1 1,SAMEA3498616,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498616|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:21|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:21,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:486 1,Beta 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,BetaCells_30000_GTCCGC_L008_R1_001.fastq.gz BetaCells_30000_GTCCGC_L008_R2_001.fastq.gz,fastq fastq,10597717092.0,52463946.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:486 1,0:101 1:101,A:2951812422;C:2213949786;G:2252957090;T:3178649938;N:347856,101,101,,,2951812422,2213949786,2252957090,3178649938,347856,ERX1054559,ERS805765,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90302,0.84857,0.12843,0.12749,0.77745,0.79157,0.56129,0.52011,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
3759,ERR1294279,ERX1365625,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9,vbu13,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu13_GCCAAT_L008_R1_001.fastq.gz,fastq,2376143675.0,23526175.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9,0:101,A:655940769;C:534990399;G:527934646;T:655773043;N:1504818,101,,,,655940769,534990399,527934646,655773043,1504818,ERX1365625,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95443,,0.10666,,0.73176,,0.50978,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3760,ERR1294278,ERX1365624,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8,vbu12,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu12_GTGAAA_L008_R1_001.fastq.gz,fastq,1449181835.0,14348335.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8,0:101,A:399518584;C:327615685;G:323868050;T:397240465;N:939051,101,,,,399518584,327615685,323868050,397240465,939051,ERX1365624,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95893,,0.09315,,0.73464,,0.48744,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3761,ERR1294277,ERX1365623,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7,vbu11,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu11_GTCCGC_L008_R1_001.fastq.gz,fastq,1455235169.0,14408269.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7,0:101,A:392100064;C:337980617;G:331091626;T:393178582;N:884280,101,,,,392100064,337980617,331091626,393178582,884280,ERX1365623,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95485,,0.08016,,0.72845,,0.47549,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3762,ERR1294276,ERX1365622,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6,ve13,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve13_CCGTCC_L008_R1_001.fastq.gz,fastq,1029294030.0,10191030.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6,0:101,A:284612731;C:231451012;G:228443320;T:284135536;N:651431,101,,,,284612731,231451012,228443320,284135536,651431,ERX1365622,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.93287,,0.10726,,0.72585,,0.4913,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3763,ERR1294275,ERX1365621,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5,ve12,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve12_ATGTCA_L008_R1_001.fastq.gz,fastq,1446322222.0,14320022.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5,0:101,A:400821160;C:324210104;G:320286425;T:400078485;N:926048,101,,,,400821160,324210104,320286425,400078485,926048,ERX1365621,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.92778,,0.09489,,0.73093,,0.48493,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3764,ERR1294274,ERX1365620,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4,ve11,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve11_AGTTCC_L008_R1_001.fastq.gz,fastq,2117238861.0,20962761.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4,0:101,A:591654664;C:469803769;G:462550117;T:591863795;N:1366516,101,,,,591654664,469803769,462550117,591863795,1366516,ERX1365620,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.93146,,0.09666,,0.73501,,0.48749,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3765,ERR1294273,ERX1365619,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3,wt3,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt3_AGTCAA_L008_R1_001.fastq.gz,fastq,2631687411.0,26056311.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3,0:101,A:734843629;C:584316000;G:577487406;T:733356850;N:1683526,101,,,,734843629,584316000,577487406,733356850,1683526,ERX1365619,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95114,,0.1036,,0.72474,,0.48261,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3766,ERR1294272,ERX1365618,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2,wt2,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt2_CTTGTA_L008_R1_001.fastq.gz,fastq,2093443463.0,20727163.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2,0:101,A:607582034;C:442802229;G:437957089;T:603752294;N:1349817,101,,,,607582034,442802229,437957089,603752294,1349817,ERX1365618,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.94792,,0.10892,,0.73277,,0.51067,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3767,ERR1294271,ERX1365617,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1,wt1,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt1_CAGATC_L008_R1_001.fastq.gz,fastq,1701561241.0,16847141.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1,0:101,A:505358711;C:348893979;G:343445186;T:502880170;N:983195,101,,,,505358711,348893979,343445186,502880170,983195,ERX1365617,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.94565,,0.13032,,0.73669,,0.50473,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
5879,ERR1759701,ERX1826022,ERS1474296,ERP020578,PRJEB18632,RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,E-MTAB-5323,Transcriptome Analysis,The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.,ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323,,Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.,Sample2,SAMEA27136168,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute,ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2,,,,,,,,,Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,E MTAB 5323:Sample2 s,Sample2 s,RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.,Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiSeq,,ERP020578,Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16,mochizukis_lab_myl7_actn2tdEos_72h_01.fastq.gz,fastq,448234901.0,6016977.0,E MTAB 5323:Sample2,0:74.50 1:0,A:118923409;C:100586009;G:99987046;T:126071553;N:2666884,74,0,,,118923409,100586009,99987046,126071553,2666884,ERX1826022,ERS1474296,ERA776061,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive,1,0.88465,,0.27583,,0.75398,,0.55917,,75,,B,,usable mapping rate,illumina,miseq,full_length,poly_a,nebnext,bulk,unknown,unknown,,Japan,2016-12-15,Larval,Larval,Heart,Cardiovascular System
5880,ERR1759702,ERX1826022,ERS1474296,ERP020578,PRJEB18632,RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,E-MTAB-5323,Transcriptome Analysis,The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.,ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323,,Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.,Sample2,SAMEA27136168,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute,ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2,,,,,,,,,Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,E MTAB 5323:Sample2 s,Sample2 s,RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.,Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiSeq,,ERP020578,Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16,mochizukis_lab_myl7_actn2tdEos_72h_02.fastq.gz,fastq,448116860.0,6016977.0,E MTAB 5323:Sample2 1,0:0 1:74.48,A:127811460;C:99875207;G:106561979;T:113792335;N:75879,0,74,,,127811460,99875207,106561979,113792335,75879,ERX1826022,ERS1474296,ERA776061,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive,1,0.91589,,0.2509,,0.79005,,0.54852,,75,,B,,usable mapping rate,illumina,miseq,full_length,poly_a,nebnext,bulk,unknown,unknown,,Japan,2016-12-15,Larval,Larval,Heart,Cardiovascular System
5881,ERR1759699,ERX1826021,ERS1474295,ERP020578,PRJEB18632,RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,E-MTAB-5323,Transcriptome Analysis,The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.,ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323,,Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.,Sample1,SAMEA27135418,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute,ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1,,,,,,,,,Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,E MTAB 5323:Sample1 s,Sample1 s,RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.,Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiSeq,,ERP020578,Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16,mochizukis_lab_myl7_NLSmCherry_72h_01.fastq.gz,fastq,766363334.0,10284347.0,E MTAB 5323:Sample1,0:74.52 1:0,A:201960096;C:174999154;G:173403690;T:211341998;N:4658396,74,0,,,201960096,174999154,173403690,211341998,4658396,ERX1826021,ERS1474295,ERA776061,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive,1,0.86003,,0.20554,,0.76301,,0.55753,,74,,B,,usable mapping rate,illumina,miseq,full_length,poly_a,nebnext,bulk,unknown,unknown,,Japan,2016-12-15,Larval,Larval,Heart,Cardiovascular System
5882,ERR1759700,ERX1826021,ERS1474295,ERP020578,PRJEB18632,RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,E-MTAB-5323,Transcriptome Analysis,The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.,ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323,,Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.,Sample1,SAMEA27135418,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute,ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1,,,,,,,,,Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,E MTAB 5323:Sample1 s,Sample1 s,RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.,Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiSeq,,ERP020578,Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf,ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16,mochizukis_lab_myl7_NLSmCHerry_72h_02.fastq.gz,fastq,766251339.0,10284347.0,E MTAB 5323:Sample1 1,0:0 1:74.51,A:214234414;C:174215653;G:180382062;T:197361982;N:57228,0,74,,,214234414,174215653,180382062,197361982,57228,ERX1826021,ERS1474295,ERA776061,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive,Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive,1,0.87766,,0.21561,,0.77477,,0.53919,,73,,B,,usable mapping rate,illumina,miseq,full_length,poly_a,nebnext,bulk,unknown,unknown,,Japan,2016-12-15,Larval,Larval,Heart,Cardiovascular System
8092,ERR2402432,ERX2443286,ERS2295360,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Hom MO rep3,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693977,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693977|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM12|common name:zebrafish|sample name:CM12|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 12,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM12.trimmed.read_1.fastq.gz CM12.trimmed.read_2.fastq.gz,fastq fastq,5384061477.0,38388598.0,ena RUN DPSQ 14 03 2018 19:09:09:420 12,0:70.70 1:69.55,A:1490429493;C:1197976503;G:1220014984;T:1475615043;N:25454,70,69,,,1490429493,1197976503,1220014984,1475615043,25454,ERX2443286,ERS2295360,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.92285,0.9206,0.06862,0.0688,0.73983,0.74566,0.4752,0.49125,76,75,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8093,ERR2402431,ERX2443285,ERS2295359,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Hom MO rep2,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693976,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693976|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM11|common name:zebrafish|sample name:CM11|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 11,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM11.trimmed.read_1.fastq.gz CM11.trimmed.read_2.fastq.gz,fastq fastq,5472085589.0,38860681.0,ena RUN DPSQ 14 03 2018 19:09:09:420 11,0:70.98 1:69.83,A:1514986213;C:1217661004;G:1240412104;T:1499000816;N:25452,70,69,,,1514986213,1217661004,1240412104,1499000816,25452,ERX2443285,ERS2295359,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.91987,0.91874,0.0693,0.07042,0.74042,0.74629,0.48229,0.49144,76,76,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8094,ERR2402430,ERX2443284,ERS2295358,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Hom MO rep1,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693975,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693975|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM10|common name:zebrafish|sample name:CM10|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 10,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM10.trimmed.read_1.fastq.gz CM10.trimmed.read_2.fastq.gz,fastq fastq,6091085806.0,43064771.0,ena RUN DPSQ 14 03 2018 19:09:09:420 10,0:71.33 1:70.11,A:1692450462;C:1348639943;G:1375433963;T:1674532019;N:29419,71,70,,,1692450462,1348639943,1375433963,1674532019,29419,ERX2443284,ERS2295358,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.92184,0.92064,0.0699,0.0704,0.74286,0.74874,0.48978,0.48997,75,73,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8095,ERR2402429,ERX2443283,ERS2295357,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Hom uninj rep3,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693974,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693974|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM9|common name:zebrafish|sample name:CM9|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 9,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM9.trimmed.read_1.fastq.gz CM9.trimmed.read_2.fastq.gz,fastq fastq,6329252570.0,45070159.0,ena RUN DPSQ 14 03 2018 19:09:09:420 9,0:70.79 1:69.64,A:1753489708;C:1407193617;G:1433449502;T:1735090181;N:29562,70,69,,,1753489708,1407193617,1433449502,1735090181,29562,ERX2443283,ERS2295357,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.91683,0.91616,0.06775,0.06825,0.75158,0.75737,0.49386,0.49199,76,75,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8096,ERR2402428,ERX2443282,ERS2295356,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Hom uninj rep2,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693973,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693973|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM8|common name:zebrafish|sample name:CM8|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 8,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM8.trimmed.read_1.fastq.gz CM8.trimmed.read_2.fastq.gz,fastq fastq,5405185494.0,38637007.0,ena RUN DPSQ 14 03 2018 19:09:09:420 8,0:70.45 1:69.44,A:1491577735;C:1206599147;G:1229354248;T:1477628006;N:26358,70,69,,,1491577735,1206599147,1229354248,1477628006,26358,ERX2443282,ERS2295356,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.91776,0.91567,0.07134,0.07241,0.7517,0.75716,0.47952,0.48745,73,73,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8097,ERR2402427,ERX2443281,ERS2295355,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Hom uninj rep1,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693972,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693972|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM7|common name:zebrafish|sample name:CM7|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 7,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM7.trimmed.read_1.fastq.gz CM7.trimmed.read_2.fastq.gz,fastq fastq,6262947202.0,44863127.0,ena RUN DPSQ 14 03 2018 19:09:09:420 7,0:70.28 1:69.32,A:1732018658;C:1394742098;G:1420957611;T:1715198292;N:30543,70,69,,,1732018658,1394742098,1420957611,1715198292,30543,ERX2443281,ERS2295355,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.91622,0.9144,0.0754,0.07588,0.74886,0.75371,0.48672,0.48471,76,76,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8098,ERR2402426,ERX2443280,ERS2295354,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Het MO rep3,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693971,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693971|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM6|common name:zebrafish|sample name:CM6|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM6.trimmed.read_1.fastq.gz CM6.trimmed.read_2.fastq.gz,fastq fastq,5819615834.0,41591499.0,ena RUN DPSQ 14 03 2018 19:09:09:420 6,0:70.47 1:69.45,A:1594833553;C:1309877713;G:1335153588;T:1579722744;N:28236,70,69,,,1594833553,1309877713,1335153588,1579722744,28236,ERX2443280,ERS2295354,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.92,0.9183,0.0573,0.05793,0.77362,0.778,0.47792,0.46987,76,75,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8099,ERR2402425,ERX2443279,ERS2295353,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Het MO rep2,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693970,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693970|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM5|common name:zebrafish|sample name:CM5|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM5.trimmed.read_1.fastq.gz CM5.trimmed.read_2.fastq.gz,fastq fastq,5573895202.0,39518227.0,ena RUN DPSQ 14 03 2018 19:09:09:420 5,0:71.02 1:70.03,A:1530297250;C:1251775796;G:1276506882;T:1515288256;N:27018,71,70,,,1530297250,1251775796,1276506882,1515288256,27018,ERX2443279,ERS2295353,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.92217,0.92081,0.06807,0.06843,0.76926,0.77441,0.45543,0.48098,76,75,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8100,ERR2402424,ERX2443278,ERS2295352,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Het MO rep1,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693969,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693969|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM4|common name:zebrafish|sample name:CM4|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM4.trimmed.read_1.fastq.gz CM4.trimmed.read_2.fastq.gz,fastq fastq,5803404091.0,41335851.0,ena RUN DPSQ 14 03 2018 19:09:09:420 4,0:70.72 1:69.67,A:1590577583;C:1305683925;G:1331895549;T:1575219146;N:27888,70,69,,,1590577583,1305683925,1331895549,1575219146,27888,ERX2443278,ERS2295352,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.9216,0.91971,0.05719,0.05738,0.77333,0.77761,0.47789,0.47244,76,74,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8101,ERR2402423,ERX2443277,ERS2295351,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Het uninj rep3,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693968,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693968|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM3|common name:zebrafish|sample name:CM3|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM3.trimmed.read_1.fastq.gz CM3.trimmed.read_2.fastq.gz,fastq fastq,5992797058.0,42390223.0,ena RUN DPSQ 14 03 2018 19:09:09:420 3,0:71.26 1:70.11,A:1639390320;C:1352082344;G:1378624207;T:1622672043;N:28144,71,70,,,1639390320,1352082344,1378624207,1622672043,28144,ERX2443277,ERS2295351,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.92104,0.92006,0.07044,0.07056,0.77506,0.78137,0.48154,0.46497,75,75,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8102,ERR2402422,ERX2443276,ERS2295350,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Het uninj rep2,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693967,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693967|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM2|common name:zebrafish|sample name:CM2|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM2.trimmed.read_2.fastq.gz CM2.trimmed.read_1.fastq.gz,fastq fastq,5611396868.0,39759688.0,ena RUN DPSQ 14 03 2018 19:09:09:420 2,0:71.11 1:70.02,A:1537234166;C:1262883447;G:1288444384;T:1522807333;N:27538,71,70,,,1537234166,1262883447,1288444384,1522807333,27538,ERX2443276,ERS2295350,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.91881,0.91733,0.06861,0.06958,0.77238,0.77883,0.48415,0.47367,76,73,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
8103,ERR2402421,ERX2443275,ERS2295349,ERP107516,PRJEB25583,The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151,Other,The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression  primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here  we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose  we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3  HetMO1 3  Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14,,Het uninj rep1,Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos,SAMEA104693966,DPSQ,ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693966|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM1|common name:zebrafish|sample name:CM1|scientific name:Danio rerio,,,,,,,,,NextSeq 500 paired end sequencing,ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP107516,NextSeq 500 paired end sequencing,ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16,CM1.trimmed.read_1.fastq.gz CM1.trimmed.read_2.fastq.gz,fastq fastq,6229432533.0,44233290.0,ena RUN DPSQ 14 03 2018 19:09:09:420 1,0:70.98 1:69.85,A:1712806281;C:1395764700;G:1423415860;T:1697416127;N:29565,70,69,,,1712806281,1395764700,1423415860,1697416127,29565,ERX2443275,ERS2295349,ERA1246315,European Nucleotide Archive,"Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom",2,0.91818,0.9169,0.07104,0.07095,0.77585,0.78066,0.47896,0.46653,56,56,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2018-03-14,Undetermined,Embryo,Blood,Hematopoietic System
9355,ERR2983453,ERX2986069,ERS2955657,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R3wL,SAMEA5147912,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147912|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R3wL|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:3|organism part:liver|sample name:E MTAB 7476:R3wL|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R3wL p,R3wL p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:liver,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAADRAAPEI-207_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAADRAAPEI-207_2.fq.gz,fastq fastq,3900536400.0,19502682.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAADRAAPEI 207 ,0:100 1:100,A:1018803847;C:926996866;G:925339368;T:1028563032;N:833287,100,100,,,1018803847,926996866,925339368,1028563032,833287,ERX2986069,ERS2955657,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.97722,0.97727,0.02792,0.02783,0.84476,0.84664,0.17004,0.16966,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Liver,Liver and Biliary System
9356,ERR2983452,ERX2986068,ERS2955656,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R3wB,SAMEA5147911,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147911|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R3wB|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:3|organism part:brain|sample name:E MTAB 7476:R3wB|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R3wB p,R3wB p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:brain,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAABRAAPEI-205_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAABRAAPEI-205_2.fq.gz,fastq fastq,3622698000.0,18113490.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAABRAAPEI 205 ,0:100 1:100,A:988454110;C:825179148;G:816134465;T:992141776;N:788501,100,100,,,988454110,825179148,816134465,992141776,788501,ERX2986068,ERS2955656,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.9287,0.92856,0.14723,0.14721,0.6928,0.69469,0.4956,0.49616,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Brain,Nervous System
9357,ERR2983451,ERX2986067,ERS2955655,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R2wG,SAMEA5147910,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147910|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R2wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:2|organism part:gonad|sample name:E MTAB 7476:R2wG|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R2wG p,R2wG p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_2.fq.gz,fastq fastq,4276100600.0,21380503.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAFRAAPEI 209 ,0:100 1:100,A:1108098396;C:1033423434;G:1019885778;T:1113782383;N:910609,100,100,,,1108098396,1033423434,1019885778,1113782383,910609,ERX2986067,ERS2955655,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.9444,0.94495,0.02624,0.02606,0.74959,0.7512,0.48453,0.48539,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Gonad,Reproductive System
9358,ERR2983450,ERX2986066,ERS2955654,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R1wL,SAMEA5147909,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147909|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R1wL|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:1|organism part:liver|sample name:E MTAB 7476:R1wL|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R1wL p,R1wL p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:liver,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAACRAAPEI-206_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAACRAAPEI-206_2.fq.gz,fastq fastq,3542921400.0,17714607.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAACRAAPEI 206 ,0:100 1:100,A:927287253;C:840581371;G:838113814;T:936174847;N:764115,100,100,,,927287253,840581371,838113814,936174847,764115,ERX2986066,ERS2955654,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.9748,0.9739,0.02815,0.02746,0.84248,0.84439,0.17403,0.17668,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Liver,Liver and Biliary System
9359,ERR2983449,ERX2986065,ERS2955653,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R1wG,SAMEA5147908,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147908|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R1wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:1|organism part:gonad|sample name:E MTAB 7476:R1wG|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R1wG p,R1wG p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_2.fq.gz,fastq fastq,3574419200.0,17872096.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAERAAPEI 208 ,0:100 1:100,A:927454175;C:863033369;G:844910972;T:938253904;N:766780,100,100,,,927454175,863033369,844910972,938253904,766780,ERX2986065,ERS2955653,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.93851,0.93973,0.02799,0.02809,0.72701,0.72914,0.48827,0.48841,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Gonad,Reproductive System
9360,ERR2983448,ERX2986064,ERS2955652,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R1wB,SAMEA5147907,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147907|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R1wB|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:1|organism part:brain|sample name:E MTAB 7476:R1wB|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R1wB p,R1wB p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:brain,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAAARAAPEI-202_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAARAAPEI-202_2.fq.gz,fastq fastq,3345687800.0,16728439.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAARAAPEI 202 ,0:100 1:100,A:879841532;C:789462135;G:789187239;T:886468300;N:728594,100,100,,,879841532,789462135,789187239,886468300,728594,ERX2986064,ERS2955652,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.96514,0.96503,0.0325,0.0326,0.78967,0.79204,0.25943,0.26683,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Brain,Nervous System
9361,ERR3011947,ERX3014407,ERS2994081,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Flutamide 2,SAMEA5186582,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186582|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 2|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:Flutamide 2 s,Flutamide 2 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:flutamide|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_Flutamide_2_R1.fastq.gz,fastq,1754963940.0,23552243.0,E MTAB 7283:Flutamide 2,0:74.51 1:0,A:455444321;C:410713896;G:385640226;T:503155736;N:9761,74,0,,,455444321,410713896,385640226,503155736,9761,ERX3014407,ERS2994081,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94351,,0.11595,,0.67483,,0.48762,,73,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9362,ERR3011946,ERX3014406,ERS2994080,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Flutamide 1,SAMEA5186581,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186581|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 1|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:Flutamide 1 s,Flutamide 1 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:flutamide|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_Flutamide_1_R1.fastq.gz,fastq,1631102863.0,21898245.0,E MTAB 7283:Flutamide 1,0:74.49 1:0,A:424378341;C:380806325;G:358128992;T:467779945;N:9260,74,0,,,424378341,380806325,358128992,467779945,9260,ERX3014406,ERS2994080,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94332,,0.11797,,0.67596,,0.48847,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9363,ERR3011945,ERX3014405,ERS2994079,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,DMSO 2,SAMEA5186580,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186580|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 2|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:DMSO 2 s,DMSO 2 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_DMSO_2_R1.fastq.gz,fastq,1811573293.0,24316929.0,E MTAB 7283:DMSO 2,0:74.50 1:0,A:470888315;C:423635861;G:396796840;T:520242179;N:10098,74,0,,,470888315,423635861,396796840,520242179,10098,ERX3014405,ERS2994079,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94219,,0.12305,,0.67184,,0.47704,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9364,ERR3011944,ERX3014404,ERS2994078,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,DMSO 1,SAMEA5186579,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186579|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 1|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:DMSO 1 s,DMSO 1 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_DMSO_1_R1.fastq.gz,fastq,1609807409.0,21611475.0,E MTAB 7283:DMSO 1,0:74.49 1:0,A:420253680;C:374436301;G:352526427;T:462581933;N:9068,74,0,,,420253680,374436301,352526427,462581933,9068,ERX3014404,ERS2994078,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94094,,0.12292,,0.67006,,0.48442,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9365,ERR3011943,ERX3014403,ERS2994077,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Cyproter1 2,SAMEA5186578,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186578|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Cyproter1 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Cyproter1 2|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:Cyproterone 2 s,Cyproterone 2 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:cyproter1|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_Cyproterone_2_R1.fastq.gz,fastq,1823142918.0,24468337.0,E MTAB 7283:Cyproterone 2,0:74.51 1:0,A:469387174;C:428783310;G:403791044;T:521171021;N:10369,74,0,,,469387174,428783310,403791044,521171021,10369,ERX3014403,ERS2994077,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.9432,,0.11718,,0.67389,,0.4768,,74,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9366,ERR3011942,ERX3014402,ERS2994076,ERP112907,PRJEB30451,Effects of anti androgenic compounds on zebrafish insulin mutants,E-MTAB-7283,Transcriptome Analysis,Aiming to identify insulin independent modulators of glucose homeostasis  we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists.  To investigate how AR antagonism mediates glucose level reduction in ins mutants  we evaluated the effects of antagonist treatment using transcriptomic studies.  RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,,Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled  water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Cyproter1 1,SAMEA5186577,Max Planck Institute for Heart and Lung Research,ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186577|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Cyproter1 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Cyproter1 1|scientific name:Danio rerio|strain:ins bns102,,,,,,,,,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,E MTAB 7283:Cyproterone 1 s,Cyproterone 1 s,Effects of anti androgenic compounds on zebrafish insulin mutants,insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water.  10 animals per sample were pooled  water was removed and Trizol was added.  Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf.  Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set  Promega to avoid contamination by genomic DNA. 3µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina,Experimental Factor: compound:cyproter1|Experimental Factor: dose:10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,ERP112907,NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants,ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18,Teja_Cyproterone_1_R1.fastq.gz,fastq,1901027130.0,25512731.0,E MTAB 7283:Cyproterone 1,0:74.51 1:0,A:487302419;C:449208827;G:422183780;T:542321577;N:10527,74,0,,,487302419,449208827,422183780,542321577,10527,ERX3014402,ERS2994076,ERA1697296,European Nucleotide Archive,European Nucleotide Archive,1,0.94427,,0.11318,,0.67294,,0.47183,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2018-12-18,Larval,Larval,Embryo Imprecise,All anatomical structures
9770,ERR5838122,ERX5487778,ERS6337138,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652584,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652584|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:05 Danio rerio adult skin 5|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:05 Danio rerio adult skin 5|sex:male|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr5.1.fastq.gz S1385Nr5.2.fastq.gz,fastq fastq,6912206316.0,34306523.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5,0:100.74 1:100.74,A:1853779551;C:1607929988;G:1658402611;T:1792045990;N:48176,100,100,,,1853779551,1607929988,1658402611,1792045990,48176,ERX5487778,ERS6337138,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.96095,0.962,0.08049,0.07821,0.70654,0.70926,0.51398,0.51064,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9771,ERR5838121,ERX5487777,ERS6337136,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652582,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652582|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:04 Danio rerio adult skin 4|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:04 Danio rerio adult skin 4|sex:male|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr4.1.fastq.gz S1385Nr4.2.fastq.gz,fastq fastq,6161942050.0,30595009.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4,0:100.70 1:100.70,A:1642716052;C:1446485458;G:1490121106;T:1582576605;N:42829,100,100,,,1642716052,1446485458,1490121106,1582576605,42829,ERX5487777,ERS6337136,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.96544,0.96564,0.07368,0.07303,0.70822,0.71092,0.50154,0.50781,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9772,ERR5838120,ERX5487776,ERS6337133,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652579,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652579|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:03 Danio rerio adult skin 3|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:03 Danio rerio adult skin 3|sex:female|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr3.1.fastq.gz S1385Nr3.2.fastq.gz,fastq fastq,7422881394.0,36866805.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3,0:100.67 1:100.67,A:1950275527;C:1768648993;G:1827362519;T:1876542858;N:51497,100,100,,,1950275527,1768648993,1827362519,1876542858,51497,ERX5487776,ERS6337133,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.97031,0.97047,0.04915,0.04817,0.71459,0.71894,0.51089,0.5097,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9773,ERR5838119,ERX5487775,ERS6337132,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652578,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652578|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:02 Danio rerio adult skin 2|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:02 Danio rerio adult skin 2|sex:female|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr2.1.fastq.gz S1385Nr2.2.fastq.gz,fastq fastq,7006718028.0,34786110.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2,0:100.71 1:100.71,A:1847371523;C:1665346769;G:1712373266;T:1781565768;N:60702,100,100,,,1847371523,1665346769,1712373266,1781565768,60702,ERX5487775,ERS6337132,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.96136,0.96039,0.05872,0.05752,0.70325,0.70674,0.46717,0.48218,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9774,ERR5838118,ERX5487774,ERS6337063,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652509,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652509|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:01 Danio rerio adult skin 1|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:01 Danio rerio adult skin 1|sex:male|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr1.1.fastq.gz S1385Nr1.2.fastq.gz,fastq fastq,6586457266.0,32719900.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1,0:100.65 1:100.65,A:1709547533;C:1593125315;G:1617088678;T:1666650824;N:44916,100,100,,,1709547533,1593125315,1617088678,1666650824,44916,ERX5487774,ERS6337063,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.9531,0.95366,0.07763,0.07567,0.71384,0.71634,0.52409,0.52475,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9831,ERR4029236,ERX4030552,ERS4513990,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF Sk 1,SAMEA6786310,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786310|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF Sk 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:skin|sample name:E MTAB 8959:ZF Sk 1|scientific name:Danio rerio|sex:male,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF Sk 1 p,ZF Sk 1 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:skin|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-Sk-1_ATTACTCG-AGGCGAAG_R1_001.fastq.gz ZF-Sk-1_ATTACTCG-AGGCGAAG_R2_001.fastq.gz,fastq fastq,4614183504.0,18310252.0,E MTAB 8959:ZF Sk 1 ATTACTCG AGGCGAAG R,0:126 1:126,A:1263161349;C:1046676688;G:1038530310;T:1265433988;N:381169,126,126,,,1263161349,1046676688,1038530310,1265433988,381169,ERX4030552,ERS4513990,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.93462,0.93416,0.10434,0.10373,0.71254,0.7162,0.4722,0.46786,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Multi-tissue,Multi-system
9832,ERR4029235,ERX4030551,ERS4513989,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF M 2,SAMEA6786309,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786309|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF M 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:muscle|sample name:E MTAB 8959:ZF M 2|scientific name:Danio rerio|sex:male,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF M 2 p,ZF M 2 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:muscle|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-M-2_ATTACTCG-TAATCTTA_R2_001.fastq.gz ZF-M-2_ATTACTCG-TAATCTTA_R1_001.fastq.gz,fastq fastq,4318736184.0,17137842.0,E MTAB 8959:ZF M 2 ATTACTCG TAATCTTA R,0:126 1:126,A:1127118469;C:1038158146;G:1022013812;T:1130979521;N:466236,126,126,,,1127118469,1038158146,1022013812,1130979521,466236,ERX4030551,ERS4513989,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.97246,0.97334,0.03723,0.03642,0.8061,0.8058,0.55712,0.55957,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Multi-tissue,Multi-system
9833,ERR4029234,ERX4030550,ERS4513988,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF L 1,SAMEA6786308,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786308|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF L 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:liver|sample name:E MTAB 8959:ZF L 1|scientific name:Danio rerio|sex:male,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF L 1 p,ZF L 1 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:liver|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-L-1_ATTACTCG-TATAGCCT_R1_001.fastq.gz ZF-L-1_ATTACTCG-TATAGCCT_R2_001.fastq.gz,fastq fastq,6531942312.0,25920406.0,E MTAB 8959:ZF L 1 ATTACTCG TATAGCCT R,0:126 1:126,A:1742074981;C:1508007466;G:1507640617;T:1773534883;N:684365,126,126,,,1742074981,1508007466,1507640617,1773534883,684365,ERX4030550,ERS4513988,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.95365,0.94664,0.057,0.05639,0.78334,0.78451,0.57079,0.57336,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Liver,Liver and Biliary System
9834,ERR4029233,ERX4030549,ERS4513987,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF H 1,SAMEA6786307,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786307|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF H 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 8959:ZF H 1|scientific name:Danio rerio|sex:male,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF H 1 p,ZF H 1 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:heart|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-H-1_ATTACTCG-CAGGACGT_R2_001.fastq.gz ZF-H-1_ATTACTCG-CAGGACGT_R1_001.fastq.gz,fastq fastq,4423848660.0,17554955.0,E MTAB 8959:ZF H 1 ATTACTCG CAGGACGT R,0:126 1:126,A:1218639096;C:1001394110;G:990248385;T:1213102170;N:464899,126,126,,,1218639096,1001394110,990248385,1213102170,464899,ERX4030549,ERS4513987,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.95192,0.95388,0.08243,0.07997,0.75678,0.75915,0.50881,0.49325,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Multi-tissue,Multi-system
9835,ERR4029232,ERX4030548,ERS4513986,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF Gi 2,SAMEA6786306,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786306|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF Gi 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:gill|sample name:E MTAB 8959:ZF Gi 2|scientific name:Danio rerio|sex:male,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF Gi 2 p,ZF Gi 2 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:gill|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-Gi-2_TCCGGAGA-TATAGCCT_R2_001.fastq.gz ZF-Gi-2_TCCGGAGA-TATAGCCT_R1_001.fastq.gz,fastq fastq,5144739264.0,20415632.0,E MTAB 8959:ZF Gi 2 TCCGGAGA TATAGCCT R,0:126 1:126,A:1417436878;C:1153901826;G:1150711944;T:1422099770;N:588846,126,126,,,1417436878,1153901826,1150711944,1422099770,588846,ERX4030548,ERS4513986,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.9241,0.92549,0.09819,0.09689,0.69282,0.69441,0.50621,0.50455,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Multi-tissue,Multi-system
9836,ERR4029231,ERX4030547,ERS4513985,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF G 1,SAMEA6786305,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786305|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF G 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:gut|sample name:E MTAB 8959:ZF G 1|scientific name:Danio rerio|sex:male,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF G 1 p,ZF G 1 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:gut|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-G-1_ATTACTCG-GTACTGAC_R1_001.fastq.gz ZF-G-1_ATTACTCG-GTACTGAC_R2_001.fastq.gz,fastq fastq,4704841764.0,18670007.0,E MTAB 8959:ZF G 1 ATTACTCG GTACTGAC R,0:126 1:126,A:1201875466;C:1104244497;G:1149324323;T:1248857914;N:539564,126,126,,,1201875466,1104244497,1149324323,1248857914,539564,ERX4030547,ERS4513985,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.95324,0.95304,0.0643,0.06517,0.67588,0.68239,0.55928,0.55357,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Liver,Liver and Biliary System
9837,ERR4029230,ERX4030546,ERS4513984,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF E 2,SAMEA6786304,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786304|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF E 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:eye|sample name:E MTAB 8959:ZF E 2|scientific name:Danio rerio|sex:male,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF E 2 p,ZF E 2 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:eye|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-E-2_TCCGGAGA-ATAGAGGC_R2_001.fastq.gz ZF-E-2_TCCGGAGA-ATAGAGGC_R1_001.fastq.gz,fastq fastq,5023188324.0,19933287.0,E MTAB 8959:ZF E 2 TCCGGAGA ATAGAGGC R,0:126 1:126,A:1387107663;C:1131488657;G:1116622956;T:1387461813;N:507235,126,126,,,1387107663,1131488657,1116622956,1387461813,507235,ERX4030546,ERS4513984,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.94348,0.94343,0.12065,0.11931,0.68509,0.68848,0.51004,0.51626,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Multi-tissue,Multi-system
9838,ERR4029229,ERX4030545,ERS4513983,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF B 1,SAMEA6786303,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786303|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF B 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:brain|sample name:E MTAB 8959:ZF B 1|scientific name:Danio rerio|sex:male,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF B 1 p,ZF B 1 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:brain|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-B-1_TCCGGAGA-CCTATCCT_R1_001.fastq.gz ZF-B-1_TCCGGAGA-CCTATCCT_R2_001.fastq.gz,fastq fastq,4581319932.0,18179841.0,E MTAB 8959:ZF B 1 TCCGGAGA CCTATCCT R,0:126 1:126,A:1290565823;C:1002821741;G:990971158;T:1296339062;N:622148,126,126,,,1290565823,1002821741,990971158,1296339062,622148,ERX4030545,ERS4513983,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.94092,0.94175,0.16309,0.16239,0.69351,0.69597,0.50407,0.5013,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Multi-tissue,Multi-system
9839,ERR4029220,ERX4030536,ERS4513974,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF L 3,SAMEA6786294,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786294|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF L 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:liver|sample name:E MTAB 8959:ZF L 3|scientific name:Danio rerio|sex:female,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF L 3 p,ZF L 3 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:liver|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-L-3_ATTACTCG-CCTATCCT_R1_001.fastq.gz ZF-L-3_ATTACTCG-CCTATCCT_R2_001.fastq.gz,fastq fastq,4015386648.0,15934074.0,E MTAB 8959:ZF L 3 ATTACTCG CCTATCCT R,0:126 1:126,A:1056740845;C:942055204;G:937642096;T:1078450107;N:498396,126,126,,,1056740845,942055204,937642096,1078450107,498396,ERX4030536,ERS4513974,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.96926,0.97065,0.03757,0.03737,0.81592,0.81742,0.30093,0.3039,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Liver,Liver and Biliary System
9840,ERR4029216,ERX4030532,ERS4513970,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF L 6,SAMEA6786290,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:15Z|External Id:SAMEA6786290|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:15Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF L 6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:liver|sample name:E MTAB 8959:ZF L 6|scientific name:Danio rerio|sex:not available,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF L 6 p,ZF L 6 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:liver|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,ZF-L-6_ATTACTCG-GGCTCTGA_R1_001.fastq.gz ZF-L-6_ATTACTCG-GGCTCTGA_R2_001.fastq.gz,fastq fastq,4678483320.0,18565410.0,E MTAB 8959:ZF L 6 ATTACTCG GGCTCTGA R,0:126 1:126,A:1222934876;C:1105593331;G:1115480454;T:1234057377;N:417282,126,126,,,1222934876,1105593331,1115480454,1234057377,417282,ERX4030532,ERS4513970,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.96734,0.97048,0.03122,0.02865,0.84293,0.84482,0.2604,0.27423,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Liver,Liver and Biliary System
9841,ERR4029215,ERX4030531,ERS4513969,ERP121186,PRJEB37848,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E-MTAB-8959,Transcriptome Analysis,The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss. Tissue types included liver  skin  muscle  heart  gut  gill  eye  brain for all three species  with additionally pyloric caeca  kidney  head kidney  and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts  FPKM  or TPM  were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16,,Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,ZF L 5,SAMEA6786289,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences",ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:15Z|External Id:SAMEA6786289|INSDC center name:CIGENE  Faculty of Biosciences  The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:15Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF L 5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:liver|sample name:E MTAB 8959:ZF L 5|scientific name:Danio rerio|sex:not available,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,E MTAB 8959:ZF L 5 p,ZF L 5 p,RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,Tissue samples of multiple types were collected from adult individuals of zebrafish  medaka  and rainbow trout. Liver tissue samples were taken in replicates of four  or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock  tanks at NIVA solbergstranda  or animal laboratory facilities zebrafish  medaka: VetBio  adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.,Experimental Factor: organism part:liver|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP121186,Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio  medaka Oryzias latipes  and rainbow trout Oncorhynchus mykiss,ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 06 19,ZF-L-5_ATTACTCG-ATAGAGGC_R1_001.fastq.gz ZF-L-5_ATTACTCG-ATAGAGGC_R2_001.fastq.gz,fastq fastq,4735140228.0,18790239.0,E MTAB 8959:ZF L 5 ATTACTCG ATAGAGGC R,0:126 1:126,A:1234730507;C:1119686445;G:1126456409;T:1253805646;N:461221,126,126,,,1234730507,1119686445,1126456409,1253805646,461221,ERX4030531,ERS4513969,ERA2508028,"CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive","CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive",2,0.96297,0.96851,0.02196,0.02241,0.86598,0.8687,0.25119,0.2498,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Norway,2020-04-16,Adult,Adult,Liver,Liver and Biliary System
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
10155,ERR5236196,ERX5039563,ERS5672247,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish WT 3,SAMEA7984965,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984965|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish WT 3 p,Zebrafish WT 3 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_WT_3_1.fastq.gz Zebrafish_WT_3_2.fastq.gz,fastq fastq,7150981594.0,23678747.0,E MTAB 10068:Zebrafish WT 3 ,0:151 1:151,A:1885053833;C:1690814929;G:1772259046;T:1802798453;N:55333,151,151,,,1885053833,1690814929,1772259046,1802798453,55333,ERX5039563,ERS5672247,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.95124,0.95221,0.08338,0.08285,0.69181,0.69256,0.46157,0.46139,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System
10156,ERR5236195,ERX5039562,ERS5672246,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish WT 2,SAMEA7984964,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984964|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish WT 2 p,Zebrafish WT 2 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_WT_2_1.fastq.gz Zebrafish_WT_2_2.fastq.gz,fastq fastq,7214044026.0,23887563.0,E MTAB 10068:Zebrafish WT 2 ,0:151 1:151,A:1902219751;C:1705162605;G:1795933407;T:1810669383;N:58880,151,151,,,1902219751,1705162605,1795933407,1810669383,58880,ERX5039562,ERS5672246,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.95311,0.95386,0.07898,0.07845,0.69045,0.69061,0.46066,0.4628,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System
10157,ERR5236194,ERX5039561,ERS5672245,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish WT 1,SAMEA7984963,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984963|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish WT 1 p,Zebrafish WT 1 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_WT_1_1.fastq.gz Zebrafish_WT_1_2.fastq.gz,fastq fastq,6632043216.0,21960408.0,E MTAB 10068:Zebrafish WT 1 ,0:151 1:151,A:1763732625;C:1547925091;G:1636588945;T:1683739270;N:57285,151,151,,,1763732625,1547925091,1636588945,1683739270,57285,ERX5039561,ERS5672245,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.9495,0.95025,0.08958,0.08856,0.68661,0.68598,0.46029,0.46171,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System