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1,938 rows where experiment.library_selection = "Oligo-dT" and technology = "unknown"

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tissue_curation >10

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devstage_curation_coarse 6

experiment.platform 4

experiment.library_strategy 4

experiment.library_layout 2

technology 1

  • unknown · 1,938 ✖

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experiment.library_selection 1

  • Oligo-dT · 1,938 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
280 280 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
281 281 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
312 312 ERR977399 ERX1054382 ERS805483 ERP011343 PRJEB10137 RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48 Other Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic…       Ductal cells R3 SAMEA3498334 GIGA-R, University of Liege ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498334|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:3|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:3|strain:Tgnkx6.1:GPF                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 3 unspecified 1 nextera XT   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011343 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16 NGS14-B703_nkx2_TCCTGAGC_L003_R1_001.fastq.gz NGS14-B703_nkx2_TCCTGAGC_L003_R2_001.fastq.gz fastq fastq 14253683247.0 70913847.0 ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 3 0:101 1:100 A:3767730088;C:2759135663;G:2772107550;T:3905748607;N:1048961339 101 100     3767730088 2759135663 2772107550 3905748607 1048961339 ERX1054382 ERS805483 ERA463457 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.74612 0.7459 0.10937 0.11122 0.81704 0.81913 0.54841 0.53764 101 100 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
313 313 ERR977398 ERX1054381 ERS805482 ERP011343 PRJEB10137 RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48 Other Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic…       Ductal cells R2 SAMEA3498333 GIGA-R, University of Liege ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498333|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:2|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:2|strain:Tgnkx6.1:GPF                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 2 unspecified 1 Truseq nano DNAsample   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011343 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16 NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R2_001.fastq.gz NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R1_001.fastq.gz fastq fastq 17434323262.0 86308531.0 ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 2 0:101 1:101 A:5014046305;C:3245710338;G:3382410145;T:5701198546;N:90957928 101 101     5014046305 3245710338 3382410145 5701198546 90957928 ERX1054381 ERS805482 ERA463457 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.87938 0.83068 0.30659 0.31351 0.80162 0.8438 0.50285 0.47987 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
314 314 ERR977397 ERX1054380 ERS805481 ERP011343 PRJEB10137 RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48 Other Background: In contrast to mammals the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate not as a result of mutual repression but through the opposite effects of Notch signaling maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals besides actors of the Notch and Wnt pathways several novel markers such as id2a. Finally we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin expressing cells. Conclusions: We have shown that in the zebrafish embryo nkx6.1+ cells are bona fide multipotent pancreatic progenitors while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse pancreatic…       Ductal cells R1 SAMEA3498332 GIGA-R, University of Liege ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498332|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:1|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:1|strain:Tgnkx6.1:GPF                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 10:18:44:269 1 unspecified 1 Truseq nano DNA sample   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011343 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16 NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R1_001.fastq.gz NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R2_001.fastq.gz fastq fastq 8147922500.0 40336250.0 ena RUN GIGA R University of Liege 05 08 2015 10:18:44:269 1 0:101 1:101 A:2422471356;C:1435392327;G:1491979725;T:2755195660;N:42883432 101 101     2422471356 1435392327 1491979725 2755195660 42883432 ERX1054380 ERS805481 ERA463457 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.85302 0.79849 0.41437 0.41711 0.83871 0.87012 0.48354 0.50046 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
315 315 ERR1675931 ERX1745976 ERS805781 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R2 1 SAMEA3498632 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498632|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:37|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:37                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 06 10 2016 15:53:35:325 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 A028_tefa_acinar_GTCCGC_L006_R1_001.fastq.gz A028_tefa_acinar_GTCCGC_L006_R2_001.fastq.gz fastq fastq 10323596830.0 51106915.0 ena RUN GIGA R University of Liege 06 10 2016 15:53:35:325 1 0:101 1:101 A:2531431314;C:2448656972;G:2434247998;T:2833404838;N:75855708 101 101     2531431314 2448656972 2434247998 2833404838 75855708 ERX1745976 ERS805781 ERA727496 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.86878 0.78451 0.03164 0.02157 0.95077 0.96161 0.52068 0.26664 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
316 316 ERR977594 ERX1054577 ERS805784 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R4 SAMEA3498635 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498635|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:40|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:40                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 19 Acinar R4 1 Truseq nano DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 NGS14-B702_Acinar4_GTGAAA_L008_R1_001.fastq.gz NGS14-B702_Acinar4_GTGAAA_L008_R2_001.fastq.gz fastq fastq 16935208936.0 83837668.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 19 0:101 1:101 A:4069193994;C:3974803883;G:4029409265;T:4779969672;N:81832122 101 101     4069193994 3974803883 4029409265 4779969672 81832122 ERX1054577 ERS805784 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.93976 0.89939 0.01468 0.01416 0.93801 0.94795 0.50718 0.50041 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
317 317 ERR977593 ERX1054576 ERS805783 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R3 SAMEA3498634 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498634|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:39|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:39                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 18 Acinar R3 1 Truseq nano DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 NGS14-B701_Acinar3_ACAGTG_L008_R1_001.fastq.gz NGS14-B701_Acinar3_ACAGTG_L008_R2_001.fastq.gz fastq fastq 15710260534.0 77773567.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 18 0:101 1:101 A:3788172647;C:3700546898;G:3749520213;T:4395516227;N:76504549 101 101     3788172647 3700546898 3749520213 4395516227 76504549 ERX1054576 ERS805783 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.95517 0.92587 0.0153 0.01529 0.91504 0.92553 0.49096 0.48449 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
318 318 ERR977592 ERX1054575 ERS805782 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R2 2 SAMEA3498633 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498633|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:38|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:38                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 17 Acinar R2 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Acinar_A028_GTCCGC_L003_R1_001.fastq.gz Acinar_A028_GTCCGC_L003_R2_001.fastq.gz fastq fastq 3461595220.0 17136610.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 17 0:101 1:101 A:847745846;C:824702298;G:830498571;T:958264119;N:384386 101 101     847745846 824702298 830498571 958264119 384386 ERX1054575 ERS805782 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.86246 0.7781 0.03038 0.02178 0.95357 0.96327 0.56719 0.35588 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
319 319 ERR977591 ERX1054574 ERS805780 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R1 2 SAMEA3498631 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498631|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:36|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:36                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:490 16 Acinar R1 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Exocrine_GTGAAA_L005_R1_001.fastq.gz Exocrine_GTGAAA_L005_R2_001.fastq.gz fastq fastq 9528535334.0 47170967.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:490 16 0:101 1:101 A:2522050794;C:2076658898;G:2097686086;T:2672752253;N:159387303 101 101     2522050794 2076658898 2097686086 2672752253 159387303 ERX1054574 ERS805780 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.48352 0.37495 0.01258 0.01002 0.94194 0.95345 0.51746 0.51938 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
320 320 ERR977590 ERX1054573 ERS805779 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Acinar cells from adults purified by FACS Acinar cells R1 1 SAMEA3498630 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498630|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:35|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:35                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:489 15 Acinar R1 1 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Exocrine_30000_GTGAAA_L008_R1_001.fastq.gz Exocrine_30000_GTGAAA_L008_R2_001.fastq.gz fastq fastq 2352127188.0 11644194.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 15 0:101 1:101 A:575791638;C:562486325;G:570096367;T:643677230;N:75628 101 101     575791638 562486325 570096367 643677230 75628 ERX1054573 ERS805779 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.96358 0.92791 0.02614 0.02577 0.91534 0.92786 0.51791 0.51855 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
321 321 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
322 322 ERR977588 ERX1054571 ERS805777 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Delta cells from adults purified by FACS Delta cells R2 SAMEA3498628 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498628|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:33|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:33                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:489 13 Delta R2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 STS2_cDNA_A085_CAGATC_L003_R1_001.fastq.gz STS2_cDNA_A085_CAGATC_L003_R2_001.fastq.gz fastq fastq 9070241774.0 44902187.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 13 0:101 1:101 A:2535637917;C:1854694115;G:1908489704;T:2770396981;N:1023057 101 101     2535637917 1854694115 1908489704 2770396981 1023057 ERX1054571 ERS805777 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.94245 0.86716 0.11229 0.13234 0.76114 0.78171 0.38511 0.43811 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
323 323 ERR977587 ERX1054570 ERS805776 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Delta cells from adults purified by FACS Delta cells R1 2 SAMEA3498627 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498627|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:32|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:32                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:489 12 Delta R1 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 SST1_A027_CCGTCC_L004_R1_001.fastq.gz SST1_A027_CCGTCC_L004_R2_001.fastq.gz fastq fastq 7937290636.0 39293518.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 12 0:101 1:101 A:2179525147;C:1634082904;G:1676353742;T:2446333583;N:995260 101 101     2179525147 1634082904 1676353742 2446333583 995260 ERX1054570 ERS805776 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.81928 0.64028 0.09426 0.0961 0.80626 0.83763 0.33992 0.39097 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
324 324 ERR977586 ERX1054569 ERS805775 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Delta cells from adults purified by FACS Delta cells R1 1 SAMEA3498626 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498626|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:31|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:31                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 11 Delta R1 1 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 SST_CCGTCC_L005_R1_001.fastq.gz SST_CCGTCC_L005_R2_001.fastq.gz fastq fastq 2808424382.0 13903091.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 11 0:101 1:101 A:745970072;C:575317830;G:590596279;T:849527061;N:47013140 101 101     745970072 575317830 590596279 849527061 47013140 ERX1054569 ERS805775 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.80308 0.60403 0.09111 0.08841 0.80582 0.84035 0.34177 0.38788 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
325 325 ERR977585 ERX1054568 ERS805774 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R3 SAMEA3498625 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498625|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:30|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:30                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 10 Alpha R3 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R1_001.fastq.gz NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R2_001.fastq.gz fastq fastq 18205394430.0 90125715.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 10 0:101 1:101 A:5028541426;C:3813667922;G:3871329588;T:5386457109;N:105398385 101 101     5028541426 3813667922 3871329588 5386457109 105398385 ERX1054568 ERS805774 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.84473 0.83714 0.12924 0.13497 0.76581 0.77928 0.43397 0.42534 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
326 326 ERR977584 ERX1054567 ERS805773 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R2 2 SAMEA3498624 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498624|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:29|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:29                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 9 Alpha R2 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 A084_Alpha2cDNA_GCCAAT_L006_R1_001.fastq.gz A084_Alpha2cDNA_GCCAAT_L006_R2_001.fastq.gz fastq fastq 8621351314.0 42679957.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 9 0:101 1:101 A:2420008540;C:1748459249;G:1778002039;T:2610255006;N:64626480 101 101     2420008540 1748459249 1778002039 2610255006 64626480 ERX1054567 ERS805773 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.8123 0.7894 0.13948 0.14682 0.76609 0.78624 0.43594 0.4281 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
327 327 ERR977583 ERX1054566 ERS805772 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R2 1 SAMEA3498623 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498623|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:28|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:28                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 8 Alpha R2 1 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Alpha_2_cDNA_A084_GCCAAT_L003_R1_001.fastq.gz Alpha_2_cDNA_A084_GCCAAT_L003_R2_001.fastq.gz fastq fastq 7447261462.0 36867631.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 8 0:101 1:101 A:2085646680;C:1521470549;G:1568678066;T:2270630726;N:835441 101 101     2085646680 1521470549 1568678066 2270630726 835441 ERX1054566 ERS805772 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.81689 0.79405 0.13796 0.14503 0.76583 0.78535 0.40729 0.42815 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
328 328 ERR977582 ERX1054565 ERS805771 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R1 2 SAMEA3498622 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498622|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:27|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:27                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:488 7 Alpha R1 2 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 A083_Alpha1cDNA_ACAGTG_L006_R1_001.fastq.gz A083_Alpha1cDNA_ACAGTG_L006_R2_001.fastq.gz fastq fastq 8598483904.0 42566752.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:488 7 0:101 1:101 A:2424152802;C:1756999772;G:1780718036;T:2571949581;N:64663713 101 101     2424152802 1756999772 1780718036 2571949581 64663713 ERX1054565 ERS805771 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.80654 0.78693 0.13676 0.14263 0.76475 0.78173 0.4476 0.44884 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
329 329 ERR977581 ERX1054564 ERS805770 ERP011346 PRJEB10140 RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55 Other We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells. ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31   Alpha cells from adults purified by FACS Alpha cells R1 1 SAMEA3498621 GIGA-R, University of Liege ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498621|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:26|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:26|strain:Tggcga:GFP; Tgins:NTR mCherry                 Illumina HiSeq 2000 paired end sequencing ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 6 Alpha R1 1 1 Truseq DNA Sample prep   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2000   ERP011346 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16 Alpha1_cDNA_A083_ACAGTG_L003_R2_001.fastq.gz Alpha1_cDNA_A083_ACAGTG_L003_R1_001.fastq.gz fastq fastq 7584054852.0 37544826.0 ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 6 0:101 1:101 A:2134120600;C:1561394450;G:1604139016;T:2283553056;N:847730 101 101     2134120600 1561394450 1604139016 2283553056 847730 ERX1054564 ERS805770 ERA463595 GIGA-R, University of Liege|European Nucleotide Archive GIGA-R, University of Liege 2 0.8102 0.79183 0.13509 0.1414 0.76459 0.77958 0.44897 0.42232 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2015-08-05 Adult Adult Undetermined Undetermined
330 330 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
331 331 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
332 332 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
333 333 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
334 334 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
9918 9918 ERR5059480 ERX4865549 ERS5523939 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     aAM 6h rep1 JD AD30 PRPN1970901   ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AD30_PRPN197090.tar.gz nanopore 3739882337.0 3148027.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 0:1188.01 A:1054501690;C:834193435;G:847423060;T:1003764152;N:0 1188       1054501690 834193435 847423060 1003764152 0 ERX4865549 ERS5523939 ERA3206712 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9919 9919 ERR5167510 ERX4972431 ERS5593364 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     cDNA WT 2hpf rep1 JD T20 PDPN191089   ENA FIRST PUBLIC:2022 07 05T12:06:34Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:34Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05         ena RUN CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1                       ERX4972431   ERA3319053 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Cleavage Embryo Undetermined Embryo Imprecise
9920 9920 ERR4330695 ERX4277529 ERS4811113 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 2h rep1 WT 2h rep1 SAMEA7050483 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-B2_PDBN005727.tar.gz fastq     ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1                       ERX4277529   ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9921 9921 ERR4327134 ERX4273968 ERS4808634 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep2 WT 4h rep2 SAMEA7048000 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AM39_PDBN042841.tar.gz nanopore 719646261.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 0:801.59 A:210217908;C:152963718;G:157393834;T:199070801;N:0 801       210217908 152963718 157393834 199070801 0 ERX4273968 ERS4808634 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9922 9922 ERR4330696 ERX4277530 ERS4811114 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep1 WT 4h rep1 JD C3 PDBN006177   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-C3_PDBN006177.tar.gz nanopore 4240799932.0 4331689.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 0:979.02 A:1229803846;C:914476674;G:943703560;T:1152815852;N:0 979       1229803846 914476674 943703560 1152815852 0 ERX4277530 ERS4811114 ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9923 9923 ERR4327135 ERX4273969 ERS4808635 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep1 WT 6h rep1 JD AC29 PDBN024889   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AC29_PDBN024889.tar.gz nanopore 1900324756.0 2013035.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 0:944.01 A:549431032;C:411510218;G:422103800;T:517279706;N:0 944       549431032 411510218 422103800 517279706 0 ERX4273969 ERS4808635 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9924 9924 ERR4326350 ERX4273208 ERS4808398 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   430 LNA 6h rep1 430 LNA 6h rep1 SAMEA7047764 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-H8_PDBN059569.tar.gz nanopore 722817654.0 657296.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 0:1099.68 A:206996491;C:157022109;G:155085437;T:203713617;N:0 1099       206996491 157022109 155085437 203713617 0 ERX4273208 ERS4808398 ERA2764399 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9925 9925 ERR4335436 ERX4282181 ERS4818366 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep2 WT 6h rep2 JD W23 PRPN039928   ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-W23_PRPN039928.tar.gz nanopore 1268761319.0 1385621.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1 0:915.66 A:366823862;C:275507684;G:284634548;T:341795225;N:0 915       366823862 275507684 284634548 341795225 0 ERX4282181 ERS4818366 ERA2769006 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9926 9926 ERR4321680 ERX4268538 ERS4808125 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 0h rep1 WT 0h rep1 JD A1 GDDN003032   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 GridION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE GridION   ERP122761 GridION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-A1_GDDN003032.tar.gz nanopore 753417826.0 698774.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 0:1078.20 A:214525685;C:165042952;G:171160615;T:202688574;N:0 1078       214525685 165042952 171160615 202688574 0 ERX4268538 ERS4808125 ERA2763718 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9951 9951 ERR5961093 ERX5601614 ERS6490233 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the same batch. Uninjected2 Uninjected2   ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14         ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 8                       ERX5601614   ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS                             illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9952 9952 ERR5961092 ERX5601613 ERS6490232 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the same batch. Uninjected1 SAMEA8805898 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 06 23|ENA last update:2021 06 23|External Id:SAMEA8805898|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 06 23T08:18:31Z|INSDC last update:2021 06 23T08:18:31Z|INSDC status:public|Submitter Id:Uninjected1|common name:zebrafish|sample name:Uninjected1                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 06 23|ENA LAST UPDATE:2021 06 23 WT1_R1_001.fastq WT1_R2_001.fastq fastq fastq 5664550800.0 18881836.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 7 0:150 1:150 A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763 150 150     1493322675 1337347146 1388414458 1444981758 484763 ERX5601613 ERS6490232 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95769 0.95822 0.04407 0.04391 0.69934 0.69958 0.4411 0.45319 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9953 9953 ERR5961096 ERX5601617 ERS6490236 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the an additional batch. Uninjected5 SAMEA8805902 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805902|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected5|common name:zebrafish|sample name:Uninjected5                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 WT5_R1_001.fastq.gz WT5_R2_001.fastq.gz fastq fastq 9088444200.0 30294814.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 0:150 1:150 A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622 150 150     2404715160 2098546919 2330441921 2254532578 207622 ERX5601617 ERS6490236 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95076 0.93857 0.06296 0.06222 0.68485 0.70047 0.47429 0.48524 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9954 9954 ERR5961095 ERX5601616 ERS6490235 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the an additional batch. Uninjected4 SAMEA8805901 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805901|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected4|common name:zebrafish|sample name:Uninjected4                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 WT4_R1_001.fastq.gz WT4_R2_001.fastq.gz fastq fastq 9222083700.0 30740279.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 10 0:150 1:150 A:2328864269;C:2117919914;G:2560286870;T:2214801519;N:211128 150 150     2328864269 2117919914 2560286870 2214801519 211128 ERX5601616 ERS6490235 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95124 0.92695 0.05122 0.05036 0.69118 0.70634 0.47769 0.47806 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9955 9955 ERR5961094 ERX5601615 ERS6490234 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae uninjected controls from the an additional batch. Uninjected3 SAMEA8805900 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805900|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected3|common name:zebrafish|sample name:Uninjected3                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 WT3_R1_001.fastq.gz WT3_R2_001.fastq.gz fastq fastq 9088444200.0 30294814.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 9 0:150 1:150 A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622 150 150     2404715160 2098546919 2330441921 2254532578 207622 ERX5601615 ERS6490234 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95071 0.93855 0.06295 0.06183 0.68511 0.70065 0.47621 0.48573 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9956 9956 ERR5961091 ERX5601612 ERS6490231 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. Cas9enzyme3 SAMEA8805897 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805897|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme3|common name:zebrafish|sample name:Cas9enzyme3                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 RNA3_R1_001.fastq RNA3_R2_001.fastq fastq fastq 5814764400.0 19382548.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 6 0:150 1:150 A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867 150 150     1550014255 1359566801 1419514658 1485169819 498867 ERX5601612 ERS6490231 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.96166 0.96182 0.04962 0.04954 0.68172 0.68144 0.45683 0.46611 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9957 9957 ERR5961090 ERX5601611 ERS6490230 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. Cas9enzyme2 SAMEA8805896 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805896|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme2|common name:zebrafish|sample name:Cas9enzyme2                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 RNA2_R1_001.fastq RNA2_R2_001.fastq fastq fastq 5927606100.0 19758687.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 5 0:150 1:150 A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534 150 150     1579767222 1387675810 1439122138 1520529396 511534 ERX5601611 ERS6490230 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.96217 0.96214 0.05174 0.05176 0.67083 0.6716 0.46772 0.47128 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9958 9958 ERR5961089 ERX5601610 ERS6490229 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage. Cas9enzyme1 SAMEA8805895 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805895|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme1|common name:zebrafish|sample name:Cas9enzyme1                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 RNA1_R1_001.fastq RNA1_R2_001.fastq fastq fastq 5738133000.0 19127110.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 4 0:150 1:150 A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691 150 150     1530616107 1342298453 1401357126 1463360623 500691 ERX5601610 ERS6490229 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95709 0.9569 0.05132 0.05149 0.68771 0.68846 0.45988 0.47329 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9959 9959 ERR5961088 ERX5601609 ERS6490228 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. Cas9mRNA3 SAMEA8805894 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805894|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA3|common name:zebrafish|sample name:Cas9mRNA3                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 PRO3_R1_001.fastq PRO3_R2_001.fastq fastq fastq 9635841900.0 32119473.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 3 0:150 1:150 A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911 150 150     2562857735 2253487693 2325345541 2493627020 523911 ERX5601609 ERS6490228 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95769 0.95696 0.05441 0.05397 0.67424 0.67407 0.46338 0.46444 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9960 9960 ERR5961087 ERX5601608 ERS6490227 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. Cas9mRNA2 SAMEA8805893 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805893|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA2|common name:zebrafish|sample name:Cas9mRNA2                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 10 21 PRO2_R1_001.fastq PRO2_R2_001.fastq fastq fastq 8990649900.0 29968833.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 2 0:150 1:150 A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619 150 150     2370044440 2140400380 2185347925 2294361536 495619 ERX5601608 ERS6490227 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95444 0.95397 0.05839 0.05842 0.67377 0.67207 0.48505 0.48043 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9961 9961 ERR5961086 ERX5601607 ERS6490226 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage. Cas9mRNA1 SAMEA8805892 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805892|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA1|common name:zebrafish|sample name:Cas9mRNA1                 Illumina HiSeq 4000 paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   ERP123184 Illumina HiSeq 4000 paired end sequencing ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 PRO1_R1_001.fastq PRO1_R2_001.fastq fastq fastq 8803789500.0 29345965.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:031 1 0:150 1:150 A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952 150 150     2318913314 2090675347 2149054140 2244296747 849952 ERX5601607 ERS6490226 ERA4417635 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.954 0.9549 0.04652 0.04639 0.70806 0.71386 0.45393 0.44921 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9962 9962 ERR4902960 ERX4769932 ERS5427208 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected. CRISPR RNAseq SAMEA7670216 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670216|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:12Z|INSDC status:public|Submitter Id:CRISPR RNAseq8|common name:zebrafish|sample name:CRISPR RNAseq8                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 WT2_R1_001.fastq.gz WT2_R2_001.fastq.gz fastq fastq 7020700500.0 23402335.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 8 0:150 1:150 A:1879937256;C:1626166066;G:1693802223;T:1820178560;N:616395 150 150     1879937256 1626166066 1693802223 1820178560 616395 ERX4769932 ERS5427208 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.92352 0.92388 0.04778 0.04768 0.6924 0.69205 0.45557 0.45865 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined
9963 9963 ERR4902959 ERX4769931 ERS5427206 ERP123184 PRJEB39643 CRISPR tools for zebrafish ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 Other Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25   RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected. CRISPR RNAseq SAMEA7670214 UNIVERSITY OF CALIFORNIA - DAVIS ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670214|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq7|common name:zebrafish|sample name:CRISPR RNAseq7                 Illumina MiSeq paired end sequencing ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina MiSeq   ERP123184 Illumina MiSeq paired end sequencing ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09 WT1_R1_001.fastq.gz WT1_R2_001.fastq.gz fastq fastq 5664550800.0 18881836.0 ena RUN UNIVERSITY OF CALIFORNIA DAVIS 02 12 2020 07:26:18:139 7 0:150 1:150 A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763 150 150     1493322675 1337347146 1388414458 1444981758 484763 ERX4769931 ERS5427206 ERA3183786 UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive UNIVERSITY OF CALIFORNIA - DAVIS 2 0.95767 0.95821 0.04411 0.04384 0.69944 0.69944 0.44168 0.45263 150 150 B B biological fallback assumption illumina miseq unknown poly_a unknown bulk unknown unknown   United States 2020-10-31 Larval Larval Undetermined Undetermined

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