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
41,DRR408245,DRX393851,DRS407176,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 3,zebrafish EN replicate 3,SAMD00529465,,sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529465,DRX393851,190326ENvsNC N703 5day;EntericNeuron;rep3,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529465,,,,3729799291.0,23985772.0,DRR408245,0:77.75 1:77.75,A:978752781;C:879988139;G:903976580;T:962122970;N:4958821,77,77,,,978752781,879988139,903976580,962122970,4958821,DRX393851,DRS407176,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
42,DRR408244,DRX393850,DRS407175,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 2,zebrafish EN replicate 2,SAMD00529464,,sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529464,DRX393850,190326ENvsNC N702 5day;EntericNeuron;rep2,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529464,,,,3315994810.0,21477755.0,DRR408244,0:77.19 1:77.20,A:873970427;C:778042505;G:798459853;T:859611841;N:5910184,77,77,,,873970427,778042505,798459853,859611841,5910184,DRX393850,DRS407175,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
43,DRR408243,DRX393849,DRS407174,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 1,zebrafish EN replicate 1,SAMD00529463,,sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529463,DRX393849,190326ENvsNC N701 5day;EntericNeuron;rep1,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529463,,,,2999501518.0,19455440.0,DRR408243,0:77.08 1:77.09,A:788053541;C:705895776;G:724185148;T:775760738;N:5606315,77,77,,,788053541,705895776,724185148,775760738,5606315,DRX393849,DRS407174,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
312,ERR977399,ERX1054382,ERS805483,ERP011343,PRJEB10137,RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48",Other,Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,Ductal cells R3,SAMEA3498334,"GIGA-R, University of Liege",ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498334|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:3|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:3|strain:Tgnkx6.1:GPF,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 3,unspecified,1,nextera XT,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011343,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16,NGS14-B703_nkx2_TCCTGAGC_L003_R1_001.fastq.gz NGS14-B703_nkx2_TCCTGAGC_L003_R2_001.fastq.gz,fastq fastq,14253683247.0,70913847.0,ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 3,0:101 1:100,A:3767730088;C:2759135663;G:2772107550;T:3905748607;N:1048961339,101,100,,,3767730088,2759135663,2772107550,3905748607,1048961339,ERX1054382,ERS805483,ERA463457,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.74612,0.7459,0.10937,0.11122,0.81704,0.81913,0.54841,0.53764,101,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
313,ERR977398,ERX1054381,ERS805482,ERP011343,PRJEB10137,RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48",Other,Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,Ductal cells R2,SAMEA3498333,"GIGA-R, University of Liege",ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498333|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:2|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:2|strain:Tgnkx6.1:GPF,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 2,unspecified,1,Truseq nano DNAsample,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011343,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16,NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R2_001.fastq.gz NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R1_001.fastq.gz,fastq fastq,17434323262.0,86308531.0,ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 2,0:101 1:101,A:5014046305;C:3245710338;G:3382410145;T:5701198546;N:90957928,101,101,,,5014046305,3245710338,3382410145,5701198546,90957928,ERX1054381,ERS805482,ERA463457,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.87938,0.83068,0.30659,0.31351,0.80162,0.8438,0.50285,0.47987,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
314,ERR977397,ERX1054380,ERS805481,ERP011343,PRJEB10137,RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48",Other,Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,Ductal cells R1,SAMEA3498332,"GIGA-R, University of Liege",ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498332|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:1|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:1|strain:Tgnkx6.1:GPF,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 1,unspecified,1,Truseq nano DNA sample,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011343,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16,NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R1_001.fastq.gz NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R2_001.fastq.gz,fastq fastq,8147922500.0,40336250.0,ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 1,0:101 1:101,A:2422471356;C:1435392327;G:1491979725;T:2755195660;N:42883432,101,101,,,2422471356,1435392327,1491979725,2755195660,42883432,ERX1054380,ERS805481,ERA463457,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.85302,0.79849,0.41437,0.41711,0.83871,0.87012,0.48354,0.50046,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
315,ERR1675931,ERX1745976,ERS805781,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R2 1,SAMEA3498632,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498632|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:37|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:37,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 06 10 2016 15:53:35:325 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,A028_tefa_acinar_GTCCGC_L006_R1_001.fastq.gz A028_tefa_acinar_GTCCGC_L006_R2_001.fastq.gz,fastq fastq,10323596830.0,51106915.0,ena RUN GIGA R  University of Liege 06 10 2016 15:53:35:325 1,0:101 1:101,A:2531431314;C:2448656972;G:2434247998;T:2833404838;N:75855708,101,101,,,2531431314,2448656972,2434247998,2833404838,75855708,ERX1745976,ERS805781,ERA727496,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.86878,0.78451,0.03164,0.02157,0.95077,0.96161,0.52068,0.26664,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
316,ERR977594,ERX1054577,ERS805784,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R4,SAMEA3498635,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498635|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:40|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:40,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 19,Acinar R4,1,Truseq nano DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B702_Acinar4_GTGAAA_L008_R1_001.fastq.gz NGS14-B702_Acinar4_GTGAAA_L008_R2_001.fastq.gz,fastq fastq,16935208936.0,83837668.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 19,0:101 1:101,A:4069193994;C:3974803883;G:4029409265;T:4779969672;N:81832122,101,101,,,4069193994,3974803883,4029409265,4779969672,81832122,ERX1054577,ERS805784,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.93976,0.89939,0.01468,0.01416,0.93801,0.94795,0.50718,0.50041,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
317,ERR977593,ERX1054576,ERS805783,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R3,SAMEA3498634,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498634|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:39|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:39,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 18,Acinar R3,1,Truseq nano DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B701_Acinar3_ACAGTG_L008_R1_001.fastq.gz NGS14-B701_Acinar3_ACAGTG_L008_R2_001.fastq.gz,fastq fastq,15710260534.0,77773567.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 18,0:101 1:101,A:3788172647;C:3700546898;G:3749520213;T:4395516227;N:76504549,101,101,,,3788172647,3700546898,3749520213,4395516227,76504549,ERX1054576,ERS805783,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.95517,0.92587,0.0153,0.01529,0.91504,0.92553,0.49096,0.48449,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
318,ERR977592,ERX1054575,ERS805782,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R2 2,SAMEA3498633,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498633|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:38|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:38,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 17,Acinar R2 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Acinar_A028_GTCCGC_L003_R1_001.fastq.gz Acinar_A028_GTCCGC_L003_R2_001.fastq.gz,fastq fastq,3461595220.0,17136610.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 17,0:101 1:101,A:847745846;C:824702298;G:830498571;T:958264119;N:384386,101,101,,,847745846,824702298,830498571,958264119,384386,ERX1054575,ERS805782,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.86246,0.7781,0.03038,0.02178,0.95357,0.96327,0.56719,0.35588,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
319,ERR977591,ERX1054574,ERS805780,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R1 2,SAMEA3498631,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498631|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:36|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:36,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 16,Acinar R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Exocrine_GTGAAA_L005_R1_001.fastq.gz Exocrine_GTGAAA_L005_R2_001.fastq.gz,fastq fastq,9528535334.0,47170967.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 16,0:101 1:101,A:2522050794;C:2076658898;G:2097686086;T:2672752253;N:159387303,101,101,,,2522050794,2076658898,2097686086,2672752253,159387303,ERX1054574,ERS805780,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.48352,0.37495,0.01258,0.01002,0.94194,0.95345,0.51746,0.51938,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
320,ERR977590,ERX1054573,ERS805779,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R1 1,SAMEA3498630,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498630|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:35|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:35,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 15,Acinar R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Exocrine_30000_GTGAAA_L008_R1_001.fastq.gz Exocrine_30000_GTGAAA_L008_R2_001.fastq.gz,fastq fastq,2352127188.0,11644194.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 15,0:101 1:101,A:575791638;C:562486325;G:570096367;T:643677230;N:75628,101,101,,,575791638,562486325,570096367,643677230,75628,ERX1054573,ERS805779,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.96358,0.92791,0.02614,0.02577,0.91534,0.92786,0.51791,0.51855,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
322,ERR977588,ERX1054571,ERS805777,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Delta cells from adults purified by FACS,Delta cells R2,SAMEA3498628,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498628|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:33|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:33,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 13,Delta R2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,STS2_cDNA_A085_CAGATC_L003_R1_001.fastq.gz STS2_cDNA_A085_CAGATC_L003_R2_001.fastq.gz,fastq fastq,9070241774.0,44902187.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 13,0:101 1:101,A:2535637917;C:1854694115;G:1908489704;T:2770396981;N:1023057,101,101,,,2535637917,1854694115,1908489704,2770396981,1023057,ERX1054571,ERS805777,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.94245,0.86716,0.11229,0.13234,0.76114,0.78171,0.38511,0.43811,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
323,ERR977587,ERX1054570,ERS805776,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Delta cells from adults purified by FACS,Delta cells R1 2,SAMEA3498627,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498627|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:32|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:32,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 12,Delta R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,SST1_A027_CCGTCC_L004_R1_001.fastq.gz SST1_A027_CCGTCC_L004_R2_001.fastq.gz,fastq fastq,7937290636.0,39293518.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 12,0:101 1:101,A:2179525147;C:1634082904;G:1676353742;T:2446333583;N:995260,101,101,,,2179525147,1634082904,1676353742,2446333583,995260,ERX1054570,ERS805776,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.81928,0.64028,0.09426,0.0961,0.80626,0.83763,0.33992,0.39097,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
324,ERR977586,ERX1054569,ERS805775,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Delta cells from adults purified by FACS,Delta cells R1 1,SAMEA3498626,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498626|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:31|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:31,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 11,Delta R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,SST_CCGTCC_L005_R1_001.fastq.gz SST_CCGTCC_L005_R2_001.fastq.gz,fastq fastq,2808424382.0,13903091.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 11,0:101 1:101,A:745970072;C:575317830;G:590596279;T:849527061;N:47013140,101,101,,,745970072,575317830,590596279,849527061,47013140,ERX1054569,ERS805775,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.80308,0.60403,0.09111,0.08841,0.80582,0.84035,0.34177,0.38788,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
325,ERR977585,ERX1054568,ERS805774,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R3,SAMEA3498625,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498625|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:30|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:30,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 10,Alpha R3,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R1_001.fastq.gz NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R2_001.fastq.gz,fastq fastq,18205394430.0,90125715.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 10,0:101 1:101,A:5028541426;C:3813667922;G:3871329588;T:5386457109;N:105398385,101,101,,,5028541426,3813667922,3871329588,5386457109,105398385,ERX1054568,ERS805774,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.84473,0.83714,0.12924,0.13497,0.76581,0.77928,0.43397,0.42534,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
326,ERR977584,ERX1054567,ERS805773,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R2 2,SAMEA3498624,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498624|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:29|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:29,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 9,Alpha R2 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,A084_Alpha2cDNA_GCCAAT_L006_R1_001.fastq.gz A084_Alpha2cDNA_GCCAAT_L006_R2_001.fastq.gz,fastq fastq,8621351314.0,42679957.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 9,0:101 1:101,A:2420008540;C:1748459249;G:1778002039;T:2610255006;N:64626480,101,101,,,2420008540,1748459249,1778002039,2610255006,64626480,ERX1054567,ERS805773,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.8123,0.7894,0.13948,0.14682,0.76609,0.78624,0.43594,0.4281,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
327,ERR977583,ERX1054566,ERS805772,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R2 1,SAMEA3498623,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498623|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:28|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:28,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 8,Alpha R2 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Alpha_2_cDNA_A084_GCCAAT_L003_R1_001.fastq.gz Alpha_2_cDNA_A084_GCCAAT_L003_R2_001.fastq.gz,fastq fastq,7447261462.0,36867631.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 8,0:101 1:101,A:2085646680;C:1521470549;G:1568678066;T:2270630726;N:835441,101,101,,,2085646680,1521470549,1568678066,2270630726,835441,ERX1054566,ERS805772,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.81689,0.79405,0.13796,0.14503,0.76583,0.78535,0.40729,0.42815,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
328,ERR977582,ERX1054565,ERS805771,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R1 2,SAMEA3498622,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498622|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:27|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:27,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 7,Alpha R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,A083_Alpha1cDNA_ACAGTG_L006_R1_001.fastq.gz A083_Alpha1cDNA_ACAGTG_L006_R2_001.fastq.gz,fastq fastq,8598483904.0,42566752.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 7,0:101 1:101,A:2424152802;C:1756999772;G:1780718036;T:2571949581;N:64663713,101,101,,,2424152802,1756999772,1780718036,2571949581,64663713,ERX1054565,ERS805771,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.80654,0.78693,0.13676,0.14263,0.76475,0.78173,0.4476,0.44884,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
329,ERR977581,ERX1054564,ERS805770,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R1 1,SAMEA3498621,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498621|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:26|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:26|strain:Tggcga:GFP; Tgins:NTR mCherry,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 6,Alpha R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Alpha1_cDNA_A083_ACAGTG_L003_R2_001.fastq.gz Alpha1_cDNA_A083_ACAGTG_L003_R1_001.fastq.gz,fastq fastq,7584054852.0,37544826.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 6,0:101 1:101,A:2134120600;C:1561394450;G:1604139016;T:2283553056;N:847730,101,101,,,2134120600,1561394450,1604139016,2283553056,847730,ERX1054564,ERS805770,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.8102,0.79183,0.13509,0.1414,0.76459,0.77958,0.44897,0.42232,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
9918,ERR5059480,ERX4865549,ERS5523939,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,aAM 6h rep1,JD AD30 PRPN1970901,,ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-AD30_PRPN197090.tar.gz,nanopore,3739882337.0,3148027.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1,0:1188.01,A:1054501690;C:834193435;G:847423060;T:1003764152;N:0,1188,,,,1054501690,834193435,847423060,1003764152,0,ERX4865549,ERS5523939,ERA3206712,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,B,,usable mapping rate,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
9920,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,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,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,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,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,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,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,ERR5961093,ERX5601614,ERS6490233,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the same batch.,Uninjected2,Uninjected2,,ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 8,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14,,,,,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 8,,,,,,,,,,,,ERX5601614,,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,,,,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9952,ERR5961092,ERX5601613,ERS6490232,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the same batch.,Uninjected1,SAMEA8805898,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 06 23|ENA last update:2021 06 23|External Id:SAMEA8805898|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 06 23T08:18:31Z|INSDC last update:2021 06 23T08:18:31Z|INSDC status:public|Submitter Id:Uninjected1|common name:zebrafish|sample name:Uninjected1,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 7,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 06 23|ENA LAST UPDATE:2021 06 23,WT1_R1_001.fastq WT1_R2_001.fastq,fastq fastq,5664550800.0,18881836.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 7,0:150 1:150,A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763,150,150,,,1493322675,1337347146,1388414458,1444981758,484763,ERX5601613,ERS6490232,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95769,0.95822,0.04407,0.04391,0.69934,0.69958,0.4411,0.45319,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9953,ERR5961096,ERX5601617,ERS6490236,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the an additional batch.,Uninjected5,SAMEA8805902,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805902|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected5|common name:zebrafish|sample name:Uninjected5,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 11,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,WT5_R1_001.fastq.gz WT5_R2_001.fastq.gz,fastq fastq,9088444200.0,30294814.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 11,0:150 1:150,A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622,150,150,,,2404715160,2098546919,2330441921,2254532578,207622,ERX5601617,ERS6490236,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95076,0.93857,0.06296,0.06222,0.68485,0.70047,0.47429,0.48524,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9954,ERR5961095,ERX5601616,ERS6490235,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the an additional batch.,Uninjected4,SAMEA8805901,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805901|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected4|common name:zebrafish|sample name:Uninjected4,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 10,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,WT4_R1_001.fastq.gz WT4_R2_001.fastq.gz,fastq fastq,9222083700.0,30740279.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 10,0:150 1:150,A:2328864269;C:2117919914;G:2560286870;T:2214801519;N:211128,150,150,,,2328864269,2117919914,2560286870,2214801519,211128,ERX5601616,ERS6490235,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95124,0.92695,0.05122,0.05036,0.69118,0.70634,0.47769,0.47806,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9955,ERR5961094,ERX5601615,ERS6490234,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the an additional batch.,Uninjected3,SAMEA8805900,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805900|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected3|common name:zebrafish|sample name:Uninjected3,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 9,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,WT3_R1_001.fastq.gz WT3_R2_001.fastq.gz,fastq fastq,9088444200.0,30294814.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 9,0:150 1:150,A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622,150,150,,,2404715160,2098546919,2330441921,2254532578,207622,ERX5601615,ERS6490234,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95071,0.93855,0.06295,0.06183,0.68511,0.70065,0.47621,0.48573,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9956,ERR5961091,ERX5601612,ERS6490231,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.,Cas9enzyme3,SAMEA8805897,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805897|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme3|common name:zebrafish|sample name:Cas9enzyme3,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,RNA3_R1_001.fastq RNA3_R2_001.fastq,fastq fastq,5814764400.0,19382548.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 6,0:150 1:150,A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867,150,150,,,1550014255,1359566801,1419514658,1485169819,498867,ERX5601612,ERS6490231,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.96166,0.96182,0.04962,0.04954,0.68172,0.68144,0.45683,0.46611,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9957,ERR5961090,ERX5601611,ERS6490230,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.,Cas9enzyme2,SAMEA8805896,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805896|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme2|common name:zebrafish|sample name:Cas9enzyme2,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,RNA2_R1_001.fastq RNA2_R2_001.fastq,fastq fastq,5927606100.0,19758687.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 5,0:150 1:150,A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534,150,150,,,1579767222,1387675810,1439122138,1520529396,511534,ERX5601611,ERS6490230,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.96217,0.96214,0.05174,0.05176,0.67083,0.6716,0.46772,0.47128,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9958,ERR5961089,ERX5601610,ERS6490229,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.,Cas9enzyme1,SAMEA8805895,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805895|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme1|common name:zebrafish|sample name:Cas9enzyme1,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,RNA1_R1_001.fastq RNA1_R2_001.fastq,fastq fastq,5738133000.0,19127110.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 4,0:150 1:150,A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691,150,150,,,1530616107,1342298453,1401357126,1463360623,500691,ERX5601610,ERS6490229,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95709,0.9569,0.05132,0.05149,0.68771,0.68846,0.45988,0.47329,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9959,ERR5961088,ERX5601609,ERS6490228,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.,Cas9mRNA3,SAMEA8805894,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805894|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA3|common name:zebrafish|sample name:Cas9mRNA3,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,PRO3_R1_001.fastq PRO3_R2_001.fastq,fastq fastq,9635841900.0,32119473.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 3,0:150 1:150,A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911,150,150,,,2562857735,2253487693,2325345541,2493627020,523911,ERX5601609,ERS6490228,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95769,0.95696,0.05441,0.05397,0.67424,0.67407,0.46338,0.46444,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9960,ERR5961087,ERX5601608,ERS6490227,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.,Cas9mRNA2,SAMEA8805893,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805893|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA2|common name:zebrafish|sample name:Cas9mRNA2,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 10 21,PRO2_R1_001.fastq PRO2_R2_001.fastq,fastq fastq,8990649900.0,29968833.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 2,0:150 1:150,A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619,150,150,,,2370044440,2140400380,2185347925,2294361536,495619,ERX5601608,ERS6490227,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95444,0.95397,0.05839,0.05842,0.67377,0.67207,0.48505,0.48043,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9961,ERR5961086,ERX5601607,ERS6490226,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.,Cas9mRNA1,SAMEA8805892,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805892|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA1|common name:zebrafish|sample name:Cas9mRNA1,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,PRO1_R1_001.fastq PRO1_R2_001.fastq,fastq fastq,8803789500.0,29345965.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 1,0:150 1:150,A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952,150,150,,,2318913314,2090675347,2149054140,2244296747,849952,ERX5601607,ERS6490226,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.954,0.9549,0.04652,0.04639,0.70806,0.71386,0.45393,0.44921,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9962,ERR4902960,ERX4769932,ERS5427208,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected.,CRISPR RNAseq,SAMEA7670216,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670216|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:12Z|INSDC status:public|Submitter Id:CRISPR RNAseq8|common name:zebrafish|sample name:CRISPR RNAseq8,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 8,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,WT2_R1_001.fastq.gz WT2_R2_001.fastq.gz,fastq fastq,7020700500.0,23402335.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 8,0:150 1:150,A:1879937256;C:1626166066;G:1693802223;T:1820178560;N:616395,150,150,,,1879937256,1626166066,1693802223,1820178560,616395,ERX4769932,ERS5427208,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.92352,0.92388,0.04778,0.04768,0.6924,0.69205,0.45557,0.45865,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9963,ERR4902959,ERX4769931,ERS5427206,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected.,CRISPR RNAseq,SAMEA7670214,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670214|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq7|common name:zebrafish|sample name:CRISPR RNAseq7,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 7,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,WT1_R1_001.fastq.gz WT1_R2_001.fastq.gz,fastq fastq,5664550800.0,18881836.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 7,0:150 1:150,A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763,150,150,,,1493322675,1337347146,1388414458,1444981758,484763,ERX4769931,ERS5427206,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95767,0.95821,0.04411,0.04384,0.69944,0.69944,0.44168,0.45263,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9964,ERR4902958,ERX4769930,ERS5427204,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.,CRISPR RNAseq,SAMEA7670212,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670212|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq6|common name:zebrafish|sample name:CRISPR RNAseq6,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,RNA3_R1_001.fastq.gz RNA3_R2_001.fastq.gz,fastq fastq,5814764400.0,19382548.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 6,0:150 1:150,A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867,150,150,,,1550014255,1359566801,1419514658,1485169819,498867,ERX4769930,ERS5427204,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.96165,0.96177,0.04961,0.04952,0.68183,0.68142,0.45636,0.46565,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9965,ERR4902957,ERX4769929,ERS5427203,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.,CRISPR RNAseq,SAMEA7670211,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670211|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq5|common name:zebrafish|sample name:CRISPR RNAseq5,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,RNA2_R1_001.fastq.gz RNA2_R2_001.fastq.gz,fastq fastq,5927606100.0,19758687.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 5,0:150 1:150,A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534,150,150,,,1579767222,1387675810,1439122138,1520529396,511534,ERX4769929,ERS5427203,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.96212,0.96213,0.0519,0.05167,0.67099,0.6715,0.46875,0.47089,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9966,ERR4902956,ERX4769928,ERS5427201,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.,CRISPR RNAseq,SAMEA7670209,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670209|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq4|common name:zebrafish|sample name:CRISPR RNAseq4,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,RNA1_R1_001.fastq.gz RNA1_R2_001.fastq.gz,fastq fastq,5738133000.0,19127110.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 4,0:150 1:150,A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691,150,150,,,1530616107,1342298453,1401357126,1463360623,500691,ERX4769928,ERS5427201,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95706,0.9569,0.05122,0.05151,0.68757,0.68822,0.46039,0.4732,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9967,ERR4902955,ERX4769927,ERS5427199,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.,CRISPR RNAseq,SAMEA7670207,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670207|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq3|common name:zebrafish|sample name:CRISPR RNAseq3,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,PRO3_R1_001.fastq.gz PRO3_R2_001.fastq.gz,fastq fastq,9635841900.0,32119473.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 3,0:150 1:150,A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911,150,150,,,2562857735,2253487693,2325345541,2493627020,523911,ERX4769927,ERS5427199,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95766,0.95695,0.05445,0.05404,0.67432,0.67403,0.46385,0.46442,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9968,ERR4902954,ERX4769926,ERS5427197,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.,CRISPR RNAseq,SAMEA7670205,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670205|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq2|common name:zebrafish|sample name:CRISPR RNAseq2,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,PRO2_R1_001.fastq.gz PRO2_R2_001.fastq.gz,fastq fastq,8990649900.0,29968833.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 2,0:150 1:150,A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619,150,150,,,2370044440,2140400380,2185347925,2294361536,495619,ERX4769926,ERS5427197,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95444,0.95393,0.05848,0.05894,0.67438,0.67255,0.4825,0.48028,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9969,ERR4902953,ERX4769925,ERS5427195,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.,CRISPR RNAseq,SAMEA7670203,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670203|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq1|common name:zebrafish|sample name:CRISPR RNAseq1,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,PRO1_R1_001.fastq.gz PRO1_R2_001.fastq.gz,fastq fastq,8803789500.0,29345965.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 1,0:150 1:150,A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952,150,150,,,2318913314,2090675347,2149054140,2244296747,849952,ERX4769925,ERS5427195,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95403,0.95489,0.04655,0.0464,0.70816,0.71403,0.45357,0.44874,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
10383,ERR8517249,ERX8083723,ERS10517669,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier control,hnRNPK 003,SAMEA12918519,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918519|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 003|common name:zebrafish|sample name:hnRNPK 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: hnRNPK 003,webin reads hnRNPK 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: hnRNPK 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,hnRNPK_003_R1.fastq.gz hnRNPK_003_R2.fastq.gz,fastq fastq,2931486932.0,19421721.0,webin reads hnRNPK 003,0:75.51 1:75.43,A:759548162;C:700272829;G:700149526;T:770783019;N:733396,75,75,,,759548162,700272829,700149526,770783019,733396,ERX8083723,ERS10517669,ERA8937191,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.9621,0.96378,0.06994,0.06876,0.68757,0.68998,0.46746,0.47041,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10384,ERR8517226,ERX8083700,ERS10517665,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier control,hnRNPK 001,SAMEA12918515,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918515|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 001|common name:zebrafish|sample name:hnRNPK 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: hnRNPK 001,webin reads hnRNPK 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: hnRNPK 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,hnRNPK_001_R1.fastq.gz hnRNPK_001_R2.fastq.gz,fastq fastq,2728299749.0,18074835.0,webin reads hnRNPK 001,0:75.51 1:75.43,A:710869412;C:649804308;G:644363972;T:722599378;N:662679,75,75,,,710869412,649804308,644363972,722599378,662679,ERX8083700,ERS10517665,ERA8936710,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96092,0.96336,0.07296,0.07144,0.68862,0.69209,0.47036,0.47104,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10385,ERR8517194,ERX8083668,ERS10517668,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,RNA control,GFP 003,SAMEA12918518,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918518|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 003|common name:zebrafish|sample name:GFP 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: GFP 003,webin reads GFP 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: GFP 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,GFP_003_R1.fastq.gz GFP_003_R2.fastq.gz,fastq fastq,2845571506.0,18850866.0,webin reads GFP 003,0:75.52 1:75.43,A:737412560;C:678774596;G:684567775;T:744108157;N:708418,75,75,,,737412560,678774596,684567775,744108157,708418,ERX8083668,ERS10517668,ERA8936242,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96279,0.96355,0.06774,0.06607,0.68864,0.69183,0.469,0.46906,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10386,ERR8517159,ERX8083633,ERS10517664,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,RNA control,GFP 001,SAMEA12918514,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918514|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 001|common name:zebrafish|sample name:GFP 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: GFP 001,webin reads GFP 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: GFP 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,GFP_001_R1.fastq.gz GFP_001_R2.fastq.gz,fastq fastq,2873485447.0,19035162.0,webin reads GFP 001,0:75.52 1:75.44,A:746120172;C:687054955;G:682142981;T:757435799;N:731540,75,75,,,746120172,687054955,682142981,757435799,731540,ERX8083633,ERS10517664,ERA8935703,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96176,0.96461,0.07014,0.06932,0.68672,0.68913,0.47006,0.46794,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10387,ERR8517115,ERX8083589,ERS10517671,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier rescue,91S hnRNPK 003,SAMEA12918521,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918521|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 003|common name:zebrafish|sample name:91S hnRNPK 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 003,webin reads 91S hnRNPK 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S hnRNPK 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_hnRNPK_003_R1.fastq.gz 91S_hnRNPK_003_R2.fastq.gz,fastq fastq,2853403405.0,18902398.0,webin reads 91S hnRNPK 003,0:75.52 1:75.44,A:739541111;C:681340573;G:681790014;T:750013318;N:718389,75,75,,,739541111,681340573,681790014,750013318,718389,ERX8083589,ERS10517671,ERA8935191,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96234,0.96429,0.0679,0.06627,0.68984,0.69126,0.46434,0.47087,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10388,ERR8517082,ERX8083556,ERS10517667,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier rescue,91S hnRNPK 001,SAMEA12918517,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918517|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 001|common name:zebrafish|sample name:91S hnRNPK 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 001,webin reads 91S hnRNPK 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S hnRNPK 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_hnRNPK_001_R1.fastq.gz 91S_hnRNPK_001_R2.fastq.gz,fastq fastq,2795603091.0,18519699.0,webin reads 91S hnRNPK 001,0:75.52 1:75.43,A:722724564;C:672552332;G:664566386;T:735058575;N:701234,75,75,,,722724564,672552332,664566386,735058575,701234,ERX8083556,ERS10517667,ERA8934579,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96307,0.96547,0.06551,0.06458,0.68714,0.68856,0.46817,0.46555,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10389,ERR8517039,ERX8083513,ERS10517670,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Toxic condition,91S GFP 003,SAMEA12918520,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918520|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 003|common name:zebrafish|sample name:91S GFP 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S GFP 003,webin reads 91S GFP 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S GFP 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_GFP_003_R1.fastq.gz 91S_GFP_003_R2.fastq.gz,fastq fastq,2946600193.0,19521826.0,webin reads 91S GFP 003,0:75.51 1:75.43,A:763284580;C:704439363;G:702989767;T:775149110;N:737373,75,75,,,763284580,704439363,702989767,775149110,737373,ERX8083513,ERS10517670,ERA8933888,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96151,0.96295,0.06621,0.06481,0.68807,0.69092,0.46928,0.46982,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10390,ERR8516998,ERX8083472,ERS10517666,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Toxic condition,91S GFP 001,SAMEA12918516,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918516|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 001|common name:zebrafish|sample name:91S GFP 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S GFP 001,webin reads 91S GFP 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S GFP 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_GFP_001_R1.fastq.gz 91S_GFP_001_R2.fastq.gz,fastq fastq,2821113913.0,18686946.0,webin reads 91S GFP 001,0:75.52 1:75.44,A:726676187;C:676899384;G:676400816;T:740427303;N:710223,75,75,,,726676187,676899384,676400816,740427303,710223,ERX8083472,ERS10517666,ERA8933211,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96147,0.96465,0.07106,0.06991,0.68822,0.69556,0.47261,0.47451,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
15504,ERR757154,ERX701784,ERS659467,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Normalization across length,SAMEA3251321,UNIVERSITY OF AMSTERDAM,ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251321|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female X|common name:zebrafish|dev stage:Adult|sample name:Female X|sex:female,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16,RID0035_003.fastq.gz,fastq,275591336.0,7611054.0,ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2,0:36.21,A:72212971;C:63331647;G:68054270;T:71992448;N:0,36,,,,72212971,63331647,68054270,71992448,0,ERX701784,ERS659467,ERA410345,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76262,,0.4273,,0.8101,,0.56676,,8,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2015-02-12,Adult,Adult,Undetermined,Undetermined
15505,ERR757153,ERX701783,ERS659466,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Normalization across length,SAMEA3251320,UNIVERSITY OF AMSTERDAM,ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251320|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female 002|common name:zebrafish|dev stage:Adult|sample name:Female 002|sex:female,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16,RID0035_006.fastq.gz,fastq,193706106.0,6343893.0,ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1,0:30.53,A:52756888;C:42895374;G:46979869;T:51073975;N:0,30,,,,52756888,42895374,46979869,51073975,0,ERX701783,ERS659466,ERA410345,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74991,,0.41319,,0.83002,,0.55823,,8,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2015-02-12,Adult,Adult,Undetermined,Undetermined
15506,ERR647638,ERX604074,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_007.fastq.gz,fastq,181485343.0,7581675.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7,0:23.94,A:49408107;C:35660562;G:44520624;T:51896050;N:0,23,,,,49408107,35660562,44520624,51896050,0,ERX604074,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75831,,0.16017,,0.90723,,0.48684,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15507,ERR647632,ERX604068,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_001.fastq.gz,fastq,158714692.0,5407747.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1,0:29.35,A:42098161;C:32991434;G:38596553;T:45028544;N:0,29,,,,42098161,32991434,38596553,45028544,0,ERX604068,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75901,,0.20293,,0.89505,,0.48215,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15508,ERR647636,ERX604072,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_005.fastq.gz,fastq,124167412.0,4838491.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5,0:25.66,A:33439510;C:24728035;G:30897675;T:35102192;N:0,25,,,,33439510,24728035,30897675,35102192,0,ERX604072,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76027,,0.17783,,0.89692,,0.48421,,30,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15509,ERR647635,ERX604071,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_004.fastq.gz,fastq,124786630.0,4701452.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4,0:26.54,A:33803418;C:24800330;G:30482560;T:35700322;N:0,26,,,,33803418,24800330,30482560,35700322,0,ERX604071,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74872,,0.18448,,0.89789,,0.50377,,12,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15510,ERR647634,ERX604070,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_003.fastq.gz,fastq,110526752.0,4078127.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3,0:27.10,A:29453167;C:22981184;G:27444083;T:30648318;N:0,27,,,,29453167,22981184,27444083,30648318,0,ERX604070,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73961,,0.1804,,0.89686,,0.50069,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15511,ERR647633,ERX604069,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_002.fastq.gz,fastq,114721515.0,4468497.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2,0:25.67,A:31387085;C:22123581;G:28270438;T:32940411;N:0,25,,,,31387085,22123581,28270438,32940411,0,ERX604069,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75767,,0.17199,,0.90118,,0.49949,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15512,ERR647645,ERX604081,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_014.fastq.gz,fastq,127742942.0,5487454.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14,0:23.28,A:35700746;C:25577569;G:31187339;T:35277288;N:0,23,,,,35700746,25577569,31187339,35277288,0,ERX604081,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72451,,0.1507,,0.91078,,0.47283,,30,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15513,ERR647644,ERX604080,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_013.fastq.gz,fastq,175319872.0,7193103.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13,0:24.37,A:48008107;C:34657005;G:43047489;T:49607271;N:0,24,,,,48008107,34657005,43047489,49607271,0,ERX604080,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75539,,0.16288,,0.90388,,0.47538,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15514,ERR647643,ERX604079,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_012.fastq.gz,fastq,177443752.0,7567733.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12,0:23.45,A:48143286;C:36300870;G:44060167;T:48939429;N:0,23,,,,48143286,36300870,44060167,48939429,0,ERX604079,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74839,,0.15018,,0.90782,,0.49076,,27,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15515,ERR647642,ERX604078,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_011.fastq.gz,fastq,163389373.0,6320373.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11,0:25.85,A:44540588;C:32608476;G:40066295;T:46174014;N:0,25,,,,44540588,32608476,40066295,46174014,0,ERX604078,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75948,,0.17375,,0.90252,,0.47536,,33,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15516,ERR647641,ERX604077,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_010.fastq.gz,fastq,128059692.0,5701206.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10,0:22.46,A:35418188;C:24802528;G:31593786;T:36245190;N:0,22,,,,35418188,24802528,31593786,36245190,0,ERX604077,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72586,,0.1331,,0.92514,,0.4216,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15517,ERR647637,ERX604073,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 6,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_006.fastq.gz,fastq,165327404.0,6835740.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 6,0:24.19,A:45252916;C:32442683;G:40306020;T:47325785;N:0,24,,,,45252916,32442683,40306020,47325785,0,ERX604073,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74944,,0.16,,0.91068,,0.47704,,21,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15518,ERR647640,ERX604076,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_009.fastq.gz,fastq,134426587.0,5846482.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9,0:22.99,A:36803811;C:26283055;G:33442229;T:37897492;N:0,22,,,,36803811,26283055,33442229,37897492,0,ERX604076,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74219,,0.13958,,0.91837,,0.47819,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15519,ERR647639,ERX604075,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_008.fastq.gz,fastq,164369360.0,6762174.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8,0:24.31,A:44826982;C:33030972;G:40615427;T:45895979;N:0,24,,,,44826982,33030972,40615427,45895979,0,ERX604075,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75513,,0.16254,,0.90534,,0.50535,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15520,ERR647623,ERX604059,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_008.fastq.gz,fastq,198146766.0,7373392.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8,0:26.87,A:50518864;C:42346985;G:50683068;T:54597849;N:0,26,,,,50518864,42346985,50683068,54597849,0,ERX604059,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73719,,0.16567,,0.89869,,0.49695,,76,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15521,ERR647622,ERX604058,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_007.fastq.gz,fastq,240260456.0,9194064.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7,0:26.13,A:62434032;C:50861577;G:60916218;T:66048629;N:0,26,,,,62434032,50861577,60916218,66048629,0,ERX604058,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73042,,0.17017,,0.89509,,0.51784,,44,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15522,ERR647620,ERX604056,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_005.fastq.gz,fastq,140470735.0,4903805.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5,0:28.65,A:35312706;C:29191443;G:36788541;T:39178045;N:0,28,,,,35312706,29191443,36788541,39178045,0,ERX604056,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76081,,0.16609,,0.90216,,0.48155,,72,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15523,ERR647617,ERX604053,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_002.fastq.gz,fastq,113953599.0,4875815.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2,0:23.37,A:29576305;C:23096908;G:29656780;T:31623606;N:0,23,,,,29576305,23096908,29656780,31623606,0,ERX604053,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70891,,0.13528,,0.91208,,0.4622,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15524,ERR647624,ERX604060,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_009.fastq.gz,fastq,127769435.0,5492615.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9,0:23.26,A:34397217;C:25332113;G:31991788;T:36048317;N:0,23,,,,34397217,25332113,31991788,36048317,0,ERX604060,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71147,,0.1472,,0.91015,,0.49014,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15525,ERR647629,ERX604065,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_014.fastq.gz,fastq,83983757.0,3823842.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14,0:21.96,A:22501534;C:16455147;G:21619305;T:23407771;N:0,21,,,,22501534,16455147,21619305,23407771,0,ERX604065,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70211,,0.13351,,0.92038,,0.45898,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15526,ERR647631,ERX604067,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_016.fastq.gz,fastq,117220472.0,4272650.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16,0:27.44,A:29509123;C:25768315;G:30220006;T:31723028;N:0,27,,,,29509123,25768315,30220006,31723028,0,ERX604067,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.68585,,0.14679,,0.90778,,0.49492,,20,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15527,ERR647618,ERX604054,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_003.fastq.gz,fastq,165279016.0,5211580.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3,0:31.71,A:41451579;C:36699133;G:41477197;T:45651107;N:0,31,,,,41451579,36699133,41477197,45651107,0,ERX604054,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71827,,0.17456,,0.90554,,0.50274,,18,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15528,ERR647621,ERX604057,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_006.fastq.gz,fastq,181164500.0,7686285.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6,0:23.57,A:48622049;C:36019225;G:45318073;T:51205153;N:0,23,,,,48622049,36019225,45318073,51205153,0,ERX604057,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73267,,0.15948,,0.9026,,0.483,,14,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15529,ERR647619,ERX604055,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_004.fastq.gz,fastq,131702671.0,4688094.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4,0:28.09,A:32537215;C:28853793;G:34317576;T:35994087;N:0,28,,,,32537215,28853793,34317576,35994087,0,ERX604055,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.68635,,0.14911,,0.90532,,0.50027,,31,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15530,ERR647628,ERX604064,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_013.fastq.gz,fastq,123881257.0,5143681.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13,0:24.08,A:32852368;C:25503683;G:31339781;T:34185425;N:0,24,,,,32852368,25503683,31339781,34185425,0,ERX604064,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72384,,0.15147,,0.90648,,0.46,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15531,ERR647627,ERX604063,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_012.fastq.gz,fastq,135155439.0,6123293.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12,0:22.07,A:35870227;C:27070386;G:34401412;T:37813414;N:0,22,,,,35870227,27070386,34401412,37813414,0,ERX604063,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.69126,,0.12647,,0.91695,,0.46572,,25,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15532,ERR647626,ERX604062,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_011.fastq.gz,fastq,138836612.0,5648801.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11,0:24.58,A:36426455;C:28359755;G:34985736;T:39064666;N:0,24,,,,36426455,28359755,34985736,39064666,0,ERX604062,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73565,,0.15718,,0.90382,,0.45772,,67,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15533,ERR647625,ERX604061,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_010.fastq.gz,fastq,182404716.0,6612019.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10,0:27.59,A:47718609;C:38775928;G:45637186;T:50272993;N:0,27,,,,47718609,38775928,45637186,50272993,0,ERX604061,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75246,,0.19746,,0.88544,,0.48212,,36,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15534,ERR647616,ERX604052,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:086 1,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_001.fastq.gz,fastq,137653436.0,5155975.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 1,0:26.70,A:34561717;C:29961559;G:35320222;T:37809938;N:0,26,,,,34561717,29961559,35320222,37809938,0,ERX604052,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71887,,0.15223,,0.90824,,0.49462,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15535,ERR647630,ERX604066,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_015.fastq.gz,fastq,101714594.0,4045987.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15,0:25.14,A:26518632;C:20741074;G:25853629;T:28601259;N:0,25,,,,26518632,20741074,25853629,28601259,0,ERX604066,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74566,,0.16455,,0.89534,,0.48977,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15536,ERR647610,ERX604046,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent PGM sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,,ERP007147,Ion Torrent PGM sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_009.fastq.gz,fastq,114880508.0,4321457.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1,0:26.58,A:31499097;C:23030789;G:27803371;T:32547251;N:0,26,,,,31499097,23030789,27803371,32547251,0,ERX604046,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.7932,,0.2086,,0.89045,,0.49364,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15537,ERR647611,ERX604047,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_010.fastq.gz,fastq,124380158.0,4885304.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2,0:25.46,A:33809369;C:25116497;G:30529372;T:34924920;N:0,25,,,,33809369,25116497,30529372,34924920,0,ERX604047,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78302,,0.1944,,0.89398,,0.50469,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15538,ERR647612,ERX604048,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_011.fastq.gz,fastq,122081664.0,4959591.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3,0:24.62,A:33452935;C:24151113;G:29942213;T:34535403;N:0,24,,,,33452935,24151113,29942213,34535403,0,ERX604048,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.77425,,0.18982,,0.8911,,0.46046,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15539,ERR647615,ERX604051,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_014.fastq.gz,fastq,120491210.0,4564333.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6,0:26.40,A:33116448;C:24416657;G:29447901;T:33510204;N:0,26,,,,33116448,24416657,29447901,33510204,0,ERX604051,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.77843,,0.20568,,0.88605,,0.51892,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15540,ERR647614,ERX604050,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_013.fastq.gz,fastq,108193052.0,4221217.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5,0:25.63,A:29795112;C:21481151;G:26281164;T:30635625;N:0,25,,,,29795112,21481151,26281164,30635625,0,ERX604050,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78861,,0.19966,,0.89207,,0.49332,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15541,ERR647613,ERX604049,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_012.fastq.gz,fastq,134807115.0,5232713.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4,0:25.76,A:37141537;C:27086121;G:32486547;T:38092910;N:0,25,,,,37141537,27086121,32486547,38092910,0,ERX604049,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78328,,0.20061,,0.88903,,0.51655,,32,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15542,ERR647603,ERX604039,ERS557923,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Female 016,SAMEA2796308,UNIVERSITY OF AMSTERDAM,Alias:Female 016|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557923|Sample Name:ERS557923|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_010.fastq.gz,fastq,186445198.0,6054478.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8,0:30.79,A:51431122;C:41043403;G:44213690;T:49756983;N:0,30,,,,51431122,41043403,44213690,49756983,0,ERX604039,ERS557923,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74649,,0.44738,,0.84254,,0.55199,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15543,ERR647602,ERX604038,ERS557922,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Female 014,SAMEA2796307,UNIVERSITY OF AMSTERDAM,Alias:Female 014|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557922|Sample Name:ERS557922|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_009.fastq.gz,fastq,199860614.0,6227225.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7,0:32.09,A:53999848;C:44698032;G:48251471;T:52911263;N:0,32,,,,53999848,44698032,48251471,52911263,0,ERX604038,ERS557922,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75262,,0.42794,,0.83619,,0.5624,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15544,ERR647601,ERX604037,ERS557921,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Female 008,SAMEA2796306,UNIVERSITY OF AMSTERDAM,Alias:Female 008|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557921|Sample Name:ERS557921|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_008.fastq.gz,fastq,190251948.0,6082600.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6,0:31.28,A:50176174;C:43027879;G:47458847;T:49589048;N:0,31,,,,50176174,43027879,47458847,49589048,0,ERX604037,ERS557921,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72654,,0.373,,0.82785,,0.52436,,25,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15545,ERR647600,ERX604036,ERS557920,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Female 007,SAMEA2796305,UNIVERSITY OF AMSTERDAM,Alias:Female 007|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557920|Sample Name:ERS557920|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_007.fastq.gz,fastq,214503694.0,6990446.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5,0:30.69,A:59354819;C:47472262;G:51306173;T:56370440;N:0,30,,,,59354819,47472262,51306173,56370440,0,ERX604036,ERS557920,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74272,,0.45587,,0.83161,,0.53444,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15546,ERR647599,ERX604035,ERS557919,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 014,SAMEA2796304,UNIVERSITY OF AMSTERDAM,Alias:Male 014|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557919|Sample Name:ERS557919|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_005.fastq.gz,fastq,235098531.0,7522781.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4,0:31.25,A:58178492;C:54009752;G:64159987;T:58750300;N:0,31,,,,58178492,54009752,64159987,58750300,0,ERX604035,ERS557919,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73752,,0.19698,,0.86665,,0.58697,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15547,ERR647598,ERX604034,ERS557918,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 011,SAMEA2796303,UNIVERSITY OF AMSTERDAM,Alias:Male 011|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557918|Sample Name:ERS557918|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_004.fastq.gz,fastq,223142261.0,6553993.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3,0:34.05,A:55488952;C:50941034;G:58123716;T:58588559;N:0,34,,,,55488952,50941034,58123716,58588559,0,ERX604034,ERS557918,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74686,,0.2139,,0.86996,,0.55375,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15548,ERR647597,ERX604033,ERS557917,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 006,SAMEA2796302,UNIVERSITY OF AMSTERDAM,Alias:Male 006|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557917|Sample Name:ERS557917|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_002.fastq.gz,fastq,166401146.0,5656405.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2,0:29.42,A:41137490;C:38824883;G:44865980;T:41572793;N:0,29,,,,41137490,38824883,44865980,41572793,0,ERX604033,ERS557917,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.69452,,0.18245,,0.87044,,0.58162,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined