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
14,DRR334977,DRX323973,DRS217313,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 28 degrees rep 3,SAMD00422597,,sample name:rRNA mock community 28 degrees rep 3|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:28|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422597,DRX323973,t28 3 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422597,,,,3791170746.0,37701921.0,DRR334977,0:100.56 1:0,A:967477491;C:926887571;G:898697642;T:998107868;N:174,100,0,,,967477491,926887571,898697642,998107868,174,DRX323973,DRS217313,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.31527,,0.06446,,0.88844,,0.62118,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
15,DRR334976,DRX323972,DRS217312,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 28 degrees rep 2,SAMD00422596,,sample name:rRNA mock community 28 degrees rep 2|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:28|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422596,DRX323972,t28 2 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422596,,,,2801693695.0,27860658.0,DRR334976,0:100.56 1:0,A:700189496;C:702936549;G:679920984;T:718646067;N:599,100,0,,,700189496,702936549,679920984,718646067,599,DRX323972,DRS217312,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.43508,,0.08819,,0.85859,,0.69447,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
16,DRR334975,DRX323971,DRS217311,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 28 degrees rep 1,SAMD00422595,,sample name:rRNA mock community 28 degrees rep 1|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:28|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422595,DRX323971,t28 1 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422595,,,,3148691934.0,31307464.0,DRR334975,0:100.57 1:0,A:785000734;C:791315678;G:766594599;T:805780465;N:458,100,0,,,785000734,791315678,766594599,805780465,458,DRX323971,DRS217311,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.37139,,0.09061,,0.94065,,0.74047,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
17,DRR334974,DRX323970,DRS217310,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 19 degrees rep 3,SAMD00422594,,sample name:rRNA mock community 19 degrees rep 3|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:19|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422594,DRX323970,t19 3 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422594,,,,2856186273.0,28400524.0,DRR334974,0:100.57 1:0,A:695685787;C:733754277;G:715270279;T:711475544;N:386,100,0,,,695685787,733754277,715270279,711475544,386,DRX323970,DRS217310,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.48152,,0.10933,,0.87105,,0.7287,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
18,DRR334973,DRX323969,DRS217309,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 19 degrees rep 2,SAMD00422593,,sample name:rRNA mock community 19 degrees rep 2|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:19|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422593,DRX323969,t19 2 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422593,,,,3199929804.0,31816971.0,DRR334973,0:100.57 1:0,A:777149590;C:825478743;G:804835148;T:792466124;N:199,100,0,,,777149590,825478743,804835148,792466124,199,DRX323969,DRS217309,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.4418,,0.10282,,0.89706,,0.74667,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
19,DRR334972,DRX323968,DRS217308,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 19 degrees rep 1,SAMD00422592,,sample name:rRNA mock community 19 degrees rep 1|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:19|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422592,DRX323968,t19 1 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422592,,,,3658675391.0,36374718.0,DRR334972,0:100.58 1:0,A:879342063;C:954687406;G:929537615;T:895107890;N:417,100,0,,,879342063,954687406,929537615,895107890,417,DRX323968,DRS217308,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.49439,,0.11691,,0.88239,,0.73925,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
20,DRR334971,DRX323967,DRS217307,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 10 degrees rep 3,SAMD00422591,,sample name:rRNA mock community 10 degrees rep 3|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:10|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422591,DRX323967,t10 3 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422591,,,,3017524690.0,30006334.0,DRR334971,0:100.56 1:0,A:771967717;C:738814269;G:712866126;T:793876235;N:343,100,0,,,771967717,738814269,712866126,793876235,343,DRX323967,DRS217307,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.33157,,0.07363,,0.9093,,0.73422,,100,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
21,DRR334970,DRX323966,DRS217306,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 10 degrees rep 2,SAMD00422590,,sample name:rRNA mock community 10 degrees rep 2|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:10|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422590,DRX323966,t10 2 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422590,,,,3115915184.0,30982336.0,DRR334970,0:100.57 1:0,A:765727966;C:794741415;G:771082024;T:784363609;N:170,100,0,,,765727966,794741415,771082024,784363609,170,DRX323966,DRS217306,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.45458,,0.10504,,0.89357,,0.749,,100,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
22,DRR334969,DRX323965,DRS217305,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 10 degrees rep 1,SAMD00422589,,sample name:rRNA mock community 10 degrees rep 1|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:10|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422589,DRX323965,t10 1 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422589,,,,3206657309.0,31883532.0,DRR334969,0:100.57 1:0,A:792874386;C:814578518;G:787469614;T:811734581;N:210,100,0,,,792874386,814578518,787469614,811734581,210,DRX323965,DRS217305,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.40156,,0.09664,,0.92898,,0.74114,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,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
15549,ERR647596,ERX604032,ERS557916,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 003,SAMEA2796301,UNIVERSITY OF AMSTERDAM,Alias:Male 003|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 01T14:38:23Z|INSDC status:public|SRA accession:ERS557916|Sample Name:ERS557916|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 1,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_001.fastq.gz,fastq,167146177.0,6380638.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1,0:26.20,A:43620211;C:36811253;G:43301042;T:43413671;N:0,26,,,,43620211,36811253,43301042,43413671,0,ERX604032,ERS557916,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70048,,0.18034,,0.88075,,0.55658,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15551,ERR647594,ERX604030,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 14:02:18:976 6,RID0011,1,,,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,RID0011_015.fastq.gz,fastq,273349184.0,9019669.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6,0:30.31,A:74069549;C:59041449;G:64551451;T:75686735;N:0,30,,,,74069549,59041449,64551451,75686735,0,ERX604030,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78759,,0.26081,,0.90989,,0.51416,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15552,ERR647589,ERX604025,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 14:02:18:976 1,RID0011,1,,,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,RID0011_010.fastq.gz,fastq,54651692.0,2000589.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 1,0:27.32,A:16624629;C:13894132;G:10557585;T:13575346;N:0,27,,,,16624629,13894132,10557585,13575346,0,ERX604025,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.11072,,0.02655,,0.97749,,0.53916,,26,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15553,ERR647590,ERX604026,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 14:02:18:976 2,RID0011,1,,,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,RID0011_011.fastq.gz,fastq,47051190.0,1414933.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 2,0:33.25,A:12984359;C:11329853;G:10330928;T:12406050;N:0,33,,,,12984359,11329853,10330928,12406050,0,ERX604026,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.36871,,0.10094,,0.9483,,0.51008,,40,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15554,ERR647592,ERX604028,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 14:02:18:976 4,RID0011,1,,,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,RID0011_013.fastq.gz,fastq,394812059.0,13329274.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 4,0:29.62,A:108705027;C:84131955;G:92090437;T:109884640;N:0,29,,,,108705027,84131955,92090437,109884640,0,ERX604028,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.65205,,0.21183,,0.91977,,0.52643,,21,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15555,ERR647593,ERX604029,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 14:02:18:976 5,RID0011,1,,,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,RID0011_014.fastq.gz,fastq,143238806.0,4225461.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 5,0:33.90,A:38374880;C:31424768;G:33687670;T:39751488;N:0,33,,,,38374880,31424768,33687670,39751488,0,ERX604029,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78469,,0.26587,,0.92178,,0.51694,,80,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15556,ERR647591,ERX604027,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 14:02:18:976 3,RID0011,1,,,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,RID0011_012.fastq.gz,fastq,55541174.0,1649692.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 3,0:33.67,A:16076639;C:14164415;G:11139997;T:14160123;N:0,33,,,,16076639,14164415,11139997,14160123,0,ERX604027,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.16692,,0.04528,,0.96384,,0.52823,,17,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
34961,SRR32588718,SRX27895233,SRS24266235,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F IE,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:inner ear|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from inner ear,C2 F2 F IE,C2 F2 F IE,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240904_152521_s2.skera.flnc.fastq.gz,fastq,93609779073.0,46650644.0,m84270 240904 152521 s2.skera.flnc.fastq.gz,0:2006.61,A:27359819621;C:19471270902;G:20218480457;T:26560208093;N:0,2006,,,,27359819621,19471270902,20218480457,26560208093,0,SRX27895233,SRS24266235,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Undetermined,Undetermined
37961,SRR1205174,SRX501301,SRS582373,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 5hr 3,GSM1357182,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 5hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357182,GSM1357182: cntl neo 5hr 3; Danio rerio; RNA Seq,GSM1357182,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357182,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_5_3.fastq.gz,fastq,1630216750.0,32604335.0,GSM1357182 r1,0:50 1:0,A:435441738;C:384703554;G:377838654;T:432163463;N:69341,50,0,,,435441738,384703554,377838654,432163463,69341,SRX501301,SRS582373,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93632,,0.20492,,0.67551,,0.50281,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37962,SRR1205173,SRX501300,SRS582372,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 5hr 2,GSM1357181,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 5hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357181,GSM1357181: cntl neo 5hr 2; Danio rerio; RNA Seq,GSM1357181,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357181,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_5_2.fastq.gz,fastq,1812797550.0,36255951.0,GSM1357181 r1,0:50 1:0,A:484800524;C:426109547;G:417833682;T:483968870;N:84927,50,0,,,484800524,426109547,417833682,483968870,84927,SRX501300,SRS582372,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93602,,0.21513,,0.67517,,0.49404,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37963,SRR1205172,SRX501299,SRS582371,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 5hr 1,GSM1357180,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 5hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357180,GSM1357180: cntl neo 5hr 1; Danio rerio; RNA Seq,GSM1357180,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357180,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_5_1.fastq.gz,fastq,1616736500.0,32334730.0,GSM1357180 r1,0:50 1:0,A:425328931;C:388105733;G:379129548;T:424100489;N:71799,50,0,,,425328931,388105733,379129548,424100489,71799,SRX501299,SRS582371,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.9361,,0.23516,,0.68091,,0.50961,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37964,SRR1205171,SRX501298,SRS582370,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 5hr 3,GSM1357179,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 5hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357179,GSM1357179: gfp neo 5hr 3; Danio rerio; RNA Seq,GSM1357179,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357179,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_5_3.fastq.gz,fastq,1856512100.0,37130242.0,GSM1357179 r1,0:50 1:0,A:492227117;C:440944515;G:431529818;T:491731276;N:79374,50,0,,,492227117,440944515,431529818,491731276,79374,SRX501298,SRS582370,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93677,,0.28732,,0.71435,,0.50496,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37965,SRR1205170,SRX501297,SRS582369,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 5hr 2,GSM1357178,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 5hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357178,GSM1357178: gfp neo 5hr 2; Danio rerio; RNA Seq,GSM1357178,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357178,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_5_2.fastq.gz,fastq,1605154400.0,32103088.0,GSM1357178 r1,0:50 1:0,A:431076570;C:373656204;G:367046732;T:433299718;N:75176,50,0,,,431076570,373656204,367046732,433299718,75176,SRX501297,SRS582369,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93022,,0.29198,,0.69656,,0.47675,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37966,SRR1205169,SRX501296,SRS582368,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 5hr 1,GSM1357177,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 5hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357177,GSM1357177: gfp neo 5hr 1; Danio rerio; RNA Seq,GSM1357177,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357177,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_5_1.fastq.gz,fastq,1902899900.0,38057998.0,GSM1357177 r1,0:50 1:0,A:511489376;C:443148505;G:433716076;T:514461324;N:84619,50,0,,,511489376,443148505,433716076,514461324,84619,SRX501296,SRS582368,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.92977,,0.29647,,0.69583,,0.48582,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37967,SRR1205168,SRX501295,SRS582367,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 3hr 3,GSM1357176,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 3hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357176,GSM1357176: cntl neo 3hr 3; Danio rerio; RNA Seq,GSM1357176,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357176,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_3_3.fastq.gz,fastq,1555198750.0,31103975.0,GSM1357176 r1,0:50 1:0,A:416734314;C:365733903;G:359113904;T:413549150;N:67479,50,0,,,416734314,365733903,359113904,413549150,67479,SRX501295,SRS582367,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93432,,0.21789,,0.67363,,0.49063,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37968,SRR1205167,SRX501294,SRS582366,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 3hr 2,GSM1357175,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 3hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357175,GSM1357175: cntl neo 3hr 2; Danio rerio; RNA Seq,GSM1357175,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357175,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_3_2.fastq.gz,fastq,1701011300.0,34020226.0,GSM1357175 r1,0:50 1:0,A:453767169;C:401144167;G:392795706;T:453224665;N:79593,50,0,,,453767169,401144167,392795706,453224665,79593,SRX501294,SRS582366,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93437,,0.19214,,0.66884,,0.48995,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37969,SRR1205166,SRX501293,SRS582365,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 3hr 1,GSM1357174,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 3hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357174,GSM1357174: cntl neo 3hr 1; Danio rerio; RNA Seq,GSM1357174,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357174,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_3_1.fastq.gz,fastq,1228792200.0,24575844.0,GSM1357174 r1,0:50 1:0,A:328509222;C:288306723;G:283185002;T:328736353;N:54900,50,0,,,328509222,288306723,283185002,328736353,54900,SRX501293,SRS582365,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93269,,0.21003,,0.66592,,0.48875,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37970,SRR1205165,SRX501292,SRS582364,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 3hr 3,GSM1357173,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 3hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357173,GSM1357173: gfp neo 3hr 3; Danio rerio; RNA Seq,GSM1357173,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357173,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_3_3.fastq.gz,fastq,1406657700.0,28133154.0,GSM1357173 r1,0:50 1:0,A:379997165;C:326224852;G:320555458;T:379818406;N:61819,50,0,,,379997165,326224852,320555458,379818406,61819,SRX501292,SRS582364,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.9327,,0.3167,,0.70709,,0.48722,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37971,SRR1205164,SRX501291,SRS582363,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 3hr 2,GSM1357172,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 3hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357172,GSM1357172: gfp neo 3hr 2; Danio rerio; RNA Seq,GSM1357172,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357172,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_3_2.fastq.gz,fastq,1409177900.0,28183558.0,GSM1357172 r1,0:50 1:0,A:377366991;C:329654609;G:322942817;T:379147506;N:65977,50,0,,,377366991,329654609,322942817,379147506,65977,SRX501291,SRS582363,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.92559,,0.27573,,0.69968,,0.48668,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37972,SRR1205163,SRX501290,SRS582362,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 3hr 1,GSM1357171,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 3hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357171,GSM1357171: gfp neo 3hr 1; Danio rerio; RNA Seq,GSM1357171,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357171,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_3_1.fastq.gz,fastq,1364255100.0,27285102.0,GSM1357171 r1,0:50 1:0,A:367031933;C:317262942;G:311363762;T:368536308;N:60155,50,0,,,367031933,317262942,311363762,368536308,60155,SRX501290,SRS582362,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93433,,0.34822,,0.70504,,0.49052,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37973,SRR1205162,SRX501289,SRS582361,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp nt 1hr 3,GSM1357170,,tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp nt 1hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357170,GSM1357170: gfp nt 1hr 3; Danio rerio; RNA Seq,GSM1357170,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357170,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_nt_1_3.fastq.gz,fastq,2032585500.0,40651710.0,GSM1357170 r1,0:50 1:0,A:540423336;C:478257444;G:470055372;T:543729414;N:119934,50,0,,,540423336,478257444,470055372,543729414,119934,SRX501289,SRS582361,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93511,,0.2696,,0.70425,,0.49291,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37974,SRR1205161,SRX501288,SRS582360,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp nt 1hr 2,GSM1357169,,tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp nt 1hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357169,GSM1357169: gfp nt 1hr 2; Danio rerio; RNA Seq,GSM1357169,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357169,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_nt_1_2.fastq.gz,fastq,1562346650.0,31246933.0,GSM1357169 r1,0:50 1:0,A:414164641;C:369142355;G:361974997;T:416978503;N:86154,50,0,,,414164641,369142355,361974997,416978503,86154,SRX501288,SRS582360,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93897,,0.31695,,0.70991,,0.50448,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37975,SRR1205160,SRX501287,SRS582359,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp nt 1hr 1,GSM1357168,,tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp nt 1hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357168,GSM1357168: gfp nt 1hr 1; Danio rerio; RNA Seq,GSM1357168,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357168,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_nt_1_1.fastq.gz,fastq,1689050050.0,33781001.0,GSM1357168 r1,0:50 1:0,A:453271567;C:394505701;G:386090706;T:455068897;N:113179,50,0,,,453271567,394505701,386090706,455068897,113179,SRX501287,SRS582359,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93627,,0.28408,,0.70585,,0.48065,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37976,SRR1205159,SRX501286,SRS582358,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 1hr 3,GSM1357167,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp neo 1hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357167,GSM1357167: gfp neo 1hr 3; Danio rerio; RNA Seq,GSM1357167,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357167,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_1_3.fastq.gz,fastq,1611919200.0,32238384.0,GSM1357167 r1,0:50 1:0,A:428150047;C:380113504;G:372605259;T:430955158;N:95232,50,0,,,428150047,380113504,372605259,430955158,95232,SRX501286,SRS582358,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.94024,,0.31287,,0.71601,,0.50103,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37977,SRR1205158,SRX501285,SRS582357,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 1hr 2,GSM1357166,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp neo 1hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357166,GSM1357166: gfp neo 1hr 2; Danio rerio; RNA Seq,GSM1357166,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357166,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_1_2.fastq.gz,fastq,1653679950.0,33073599.0,GSM1357166 r1,0:50 1:0,A:439492851;C:388625865;G:381772828;T:443698911;N:89495,50,0,,,439492851,388625865,381772828,443698911,89495,SRX501285,SRS582357,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.94345,,0.38847,,0.7357,,0.50373,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37978,SRR1205157,SRX501284,SRS582356,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 1hr 1,GSM1357165,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp neo 1hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357165,GSM1357165: gfp neo 1hr 1; Danio rerio; RNA Seq,GSM1357165,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357165,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_1_1.fastq.gz,fastq,1873022200.0,37460444.0,GSM1357165 r1,0:50 1:0,A:501397145;C:438845045;G:428481612;T:504171995;N:126403,50,0,,,501397145,438845045,428481612,504171995,126403,SRX501284,SRS582356,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.933,,0.24769,,0.70591,,0.50587,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37979,SRR1205156,SRX501283,SRS582355,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl nt 1hr 3,GSM1357164,,tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl nt 1hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357164,GSM1357164: cntl nt 1hr 3; Danio rerio; RNA Seq,GSM1357164,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357164,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_nt_1_3.fastq.gz,fastq,1523970250.0,30479405.0,GSM1357164 r1,0:50 1:0,A:404458518;C:360948466;G:353690676;T:404782977;N:89613,50,0,,,404458518,360948466,353690676,404782977,89613,SRX501283,SRS582355,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93995,,0.21232,,0.66772,,0.48499,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37980,SRR1205155,SRX501282,SRS582354,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl nt 1hr 2,GSM1357163,,tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl nt 1hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357163,GSM1357163: cntl nt 1hr 2; Danio rerio; RNA Seq,GSM1357163,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357163,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_nt_1_2.fastq.gz,fastq,1649622150.0,32992443.0,GSM1357163 r1,0:50 1:0,A:434980357;C:392949654;G:385359402;T:436242531;N:90206,50,0,,,434980357,392949654,385359402,436242531,90206,SRX501282,SRS582354,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.94128,,0.24395,,0.67549,,0.50787,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37981,SRR1205154,SRX501281,SRS582353,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl nt 1hr 1,GSM1357162,,tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl nt 1hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357162,GSM1357162: cntl nt 1hr 1; Danio rerio; RNA Seq,GSM1357162,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357162,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_nt_1_1.fastq.gz,fastq,1953710600.0,39074212.0,GSM1357162 r1,0:50 1:0,A:518489677;C:462970545;G:452495723;T:519623507;N:131148,50,0,,,518489677,462970545,452495723,519623507,131148,SRX501281,SRS582353,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93818,,0.2175,,0.66229,,0.50468,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37982,SRR1205153,SRX501280,SRS582352,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 1hr 3,GSM1357161,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl neo 1hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357161,GSM1357161: cntl neo 1hr 3; Danio rerio; RNA Seq,GSM1357161,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357161,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_1_3.fastq.gz,fastq,1934085200.0,38681704.0,GSM1357161 r1,0:50 1:0,A:513203802;C:458221455;G:449581302;T:512967391;N:111250,50,0,,,513203802,458221455,449581302,512967391,111250,SRX501280,SRS582352,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93811,,0.22613,,0.66671,,0.49681,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37983,SRR1205152,SRX501279,SRS582351,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 1hr 2,GSM1357160,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl neo 1hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357160,GSM1357160: cntl neo 1hr 2; Danio rerio; RNA Seq,GSM1357160,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357160,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_1_2.fastq.gz,fastq,1836127900.0,36722558.0,GSM1357160 r1,0:50 1:0,A:485828745;C:436091545;G:426562682;T:487543575;N:101353,50,0,,,485828745,436091545,426562682,487543575,101353,SRX501279,SRS582351,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93856,,0.23223,,0.67154,,0.5021,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37984,SRR1205151,SRX501278,SRS582350,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 1hr 1,GSM1357159,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl neo 1hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357159,GSM1357159: cntl neo 1hr 1; Danio rerio; RNA Seq,GSM1357159,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357159,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_1_1.fastq.gz,fastq,1687481850.0,33749637.0,GSM1357159 r1,0:50 1:0,A:448529802;C:398804686;G:391019451;T:449013498;N:114413,50,0,,,448529802,398804686,391019451,449013498,114413,SRX501278,SRS582350,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93698,,0.21557,,0.66436,,0.49756,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
41420,SRR4423116,SRX2245300,SRS1745858,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,egg pools from three different mothers,,Egg pool Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Egg pool,94 4,94 4,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,eggRID0094BC04smallZF.fastq,fastq,1392075126.0,18333358.0,eggRID0094BC04smallZF.fastq,0:75.93,A:323480979;C:386272283;G:377777594;T:304544270;N:0,75,,,,323480979,386272283,377777594,304544270,0,SRX2245300,SRS1745858,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.68028,,0.1685,,0.89982,,0.84521,,83,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Undetermined,Undetermined,Undetermined,Undetermined
41422,SRR4423114,SRX2245298,SRS1745858,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,egg pools from three different mothers,,Egg pool Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: Egg pool,99 6,99 6,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,eggRID0099BC06LargeZF.fastq,fastq,4454090954.0,48098559.0,eggRID0099BC06LargeZF.fastq,0:92.60,A:1084275872;C:1151665265;G:1338679196;T:879470621;N:0,92,,,,1084275872,1151665265,1338679196,879470621,0,SRX2245298,SRS1745858,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.91346,,0.27222,,0.96694,,0.91118,,144,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Undetermined,Undetermined,Undetermined,Undetermined
41424,SRR4423112,SRX2245296,SRS1745858,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,egg pools from three different mothers,,Egg pool Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Egg pool,88 4,88 4,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,eggRID0088BC04smallZF.fastq,fastq,1063934659.0,14422089.0,eggRID0088BC04smallZF.fastq,0:73.77,A:248885216;C:293368431;G:288043879;T:233637133;N:0,73,,,,248885216,293368431,288043879,233637133,0,SRX2245296,SRS1745858,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.66115,,0.18031,,0.89546,,0.78468,,72,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Undetermined,Undetermined,Undetermined,Undetermined
41426,SRR4423110,SRX2245294,SRS1745858,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,egg pools from three different mothers,,Egg pool Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Egg pool,93 4,93 4,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,eggRID0093BC04smallZF.fastq,fastq,1382951404.0,18190154.0,eggRID0093BC04smallZF.fastq,0:76.03,A:322536095;C:383176934;G:374216039;T:303022336;N:0,76,,,,322536095,383176934,374216039,303022336,0,SRX2245294,SRS1745858,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.66399,,0.17461,,0.90134,,0.82432,,156,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Undetermined,Undetermined,Undetermined,Undetermined
50533,SRR8129704,SRX4950826,SRS3993016,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNeasy sorted 2,GSM3449965,,tissue:Fli:GFP  sorted  3 days  RNeasy sample 1|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,RNeasy sorted 2,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNeasy sample 1,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,GSM3449965,GSM3449965: RNeasy sorted 2; Danio rerio; RNA Seq,GSM3449965,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449965,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP167139,,,Q_1.fastq.gz,fastq,1059463914.0,14029229.0,GSM3449965 r1,0:75.52 1:0,A:284634446;C:242976410;G:245781627;T:286026099;N:45332,75,0,,,284634446,242976410,245781627,286026099,45332,SRX4950826,SRS3993016,SRA800291,GEO,"Center for Medical Genetics, Ghent University",1,0.91903,,0.09754,,0.73537,,0.48738,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
50534,SRR8129703,SRX4950825,SRS3993017,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNAqueous sorted 1,GSM3449964,,tissue:Fli:GFP  sorted  3 days  RNAqueous  sample 1|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,RNAqueous sorted 1,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNAqueous  sample 1,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,GSM3449964,GSM3449964: RNAqueous sorted 1; Danio rerio; RNA Seq,GSM3449964,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449964,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP167139,,,A_1.fastq.gz,fastq,1477268521.0,19562904.0,GSM3449964 r1,0:75.51 1:0,A:399601730;C:333778207;G:337372866;T:406448608;N:67110,75,0,,,399601730,333778207,337372866,406448608,67110,SRX4950825,SRS3993017,SRA800291,GEO,"Center for Medical Genetics, Ghent University",1,0.90617,,0.09373,,0.74558,,0.49316,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
51017,SRR8435109,SRX5242689,SRS4245412,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ f Dex+ LREs 3,GSM3560348,,tissue:cldn15la GFP+ f Dex+ LREs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,cldn15la GFP+ f Dex+ LREs 3,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ f Dex+ LREs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,GSM3560348,GSM3560348: cldn15la GFP+ f Dex+ LREs 3; Danio rerio; RNA Seq,GSM3560348,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560348,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,LRE_3.fastq.gz,fastq,3319359633.0,65085483.0,GSM3560348 r1,0:51 1:0,A:939171958;C:728294535;G:735458210;T:914956028;N:1478902,51,0,,,939171958,728294535,735458210,914956028,1478902,SRX5242689,SRS4245412,SRA833636,GEO,Duke University,1,0.92838,,0.08491,,0.73507,,0.45124,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51018,SRR8435108,SRX5242688,SRS4245413,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ f Dex+ LREs 2,GSM3560347,,tissue:cldn15la GFP+ f Dex+ LREs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,cldn15la GFP+ f Dex+ LREs 2,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ f Dex+ LREs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,GSM3560347,GSM3560347: cldn15la GFP+ f Dex+ LREs 2; Danio rerio; RNA Seq,GSM3560347,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560347,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,LRE_2.fastq.gz,fastq,3886795782.0,76211682.0,GSM3560347 r1,0:51 1:0,A:1104818772;C:851405074;G:855078243;T:1073758670;N:1735023,51,0,,,1104818772,851405074,855078243,1073758670,1735023,SRX5242688,SRS4245413,SRA833636,GEO,Duke University,1,0.9367,,0.08433,,0.73565,,0.60818,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51019,SRR8435107,SRX5242687,SRS4245410,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ f Dex+ LREs 1,GSM3560346,,tissue:cldn15la GFP+ f Dex+ LREs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,cldn15la GFP+ f Dex+ LREs 1,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ f Dex+ LREs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,GSM3560346,GSM3560346: cldn15la GFP+ f Dex+ LREs 1; Danio rerio; RNA Seq,GSM3560346,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560346,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,LRE_1.fastq.gz,fastq,3052804104.0,59858904.0,GSM3560346 r1,0:51 1:0,A:886286208;C:657679423;G:656279895;T:852223208;N:335370,51,0,,,886286208,657679423,656279895,852223208,335370,SRX5242687,SRS4245410,SRA833636,GEO,Duke University,1,0.92375,,0.09247,,0.77449,,0.67251,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51020,SRR8435106,SRX5242686,SRS4245411,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ IECs 3,GSM3560345,,tissue:cldn15la GFP+ IECs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,cldn15la GFP+ IECs 3,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ IECs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,GSM3560345,GSM3560345: cldn15la GFP+ IECs 3; Danio rerio; RNA Seq,GSM3560345,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560345,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,IEC_3.fastq.gz,fastq,3411376434.0,66889734.0,GSM3560345 r1,0:51 1:0,A:962628477;C:748798542;G:754301765;T:944119253;N:1528397,51,0,,,962628477,748798542,754301765,944119253,1528397,SRX5242686,SRS4245411,SRA833636,GEO,Duke University,1,0.92544,,0.11398,,0.71125,,0.50352,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51021,SRR8435105,SRX5242685,SRS4245408,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ IECs 2,GSM3560344,,tissue:cldn15la GFP+ IECs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,cldn15la GFP+ IECs 2,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ IECs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,GSM3560344,GSM3560344: cldn15la GFP+ IECs 2; Danio rerio; RNA Seq,GSM3560344,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560344,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,IEC_2.fastq.gz,fastq,4165555866.0,81677566.0,GSM3560344 r1,0:51 1:0,A:1164142809;C:924263682;G:930812689;T:1144479148;N:1857538,51,0,,,1164142809,924263682,930812689,1144479148,1857538,SRX5242685,SRS4245408,SRA833636,GEO,Duke University,1,0.92974,,0.09982,,0.7167,,0.5209,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51022,SRR8435104,SRX5242684,SRS4245409,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ IECs 1,GSM3560343,,tissue:cldn15la GFP+ IECs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,cldn15la GFP+ IECs 1,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ IECs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,GSM3560343,GSM3560343: cldn15la GFP+ IECs 1; Danio rerio; RNA Seq,GSM3560343,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560343,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,IEC_1.fastq.gz,fastq,3258191610.0,63886110.0,GSM3560343 r1,0:51 1:0,A:941514468;C:707367673;G:717548605;T:891005627;N:755237,51,0,,,941514468,707367673,717548605,891005627,755237,SRX5242684,SRS4245409,SRA833636,GEO,Duke University,1,0.91133,,0.12919,,0.76274,,0.60572,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
67975,SRR17547553,SRX13717013,SRS11594777,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 4 [Sus stress 9],GSM5800168,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 4 [Sus stress 9],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800168,GSM5800168: Susceptible stressed 4 [Sus stress 9]; Danio rerio; RNA Seq,GSM5800168 r1,GSM5800168,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_9_S20_L001_R1_001.fastq.gz,fastq,493772580.0,5878245.0,GSM5800168 r1,0:84 1:0,A:128397756;C:115517535;G:120125116;T:129730356;N:1817,84,0,,,128397756,115517535,120125116,129730356,1817,SRX13717013,SRS11594777,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.94974,,0.09483,,0.66448,,0.48897,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67976,SRR17547554,SRX13717013,SRS11594777,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 4 [Sus stress 9],GSM5800168,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 4 [Sus stress 9],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800168,GSM5800168: Susceptible stressed 4 [Sus stress 9]; Danio rerio; RNA Seq,GSM5800168 r1,GSM5800168,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_9_S20_L002_R1_001.fastq.gz,fastq,493766280.0,5878170.0,GSM5800168 r2,0:84 1:0,A:128477502;C:115522900;G:119992333;T:129772804;N:741,84,0,,,128477502,115522900,119992333,129772804,741,SRX13717013,SRS11594777,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.9505,,0.09356,,0.66523,,0.48634,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined