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
95,DRR050167,DRX045209,DRS025834,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 3,SAMD00044057,,sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044057,DRX045209,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044057,,,,371748120.0,3469843.0,DRR050167,0:107.14,A:107190409;C:79475572;G:83520360;T:101561779;N:0,107,,,,107190409,79475572,83520360,101561779,0,DRX045209,DRS025834,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.81026,,0.26715,,0.86953,,0.52321,,51,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
96,DRR050166,DRX045208,DRS025833,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 2,SAMD00044056,,sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044056,DRX045208,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044056,,,,425549011.0,3275261.0,DRR050166,0:129.93,A:126640704;C:86415371;G:90822163;T:121670773;N:0,129,,,,126640704,86415371,90822163,121670773,0,DRX045208,DRS025833,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.80223,,0.31429,,0.85861,,0.5272,,57,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
97,DRR050165,DRX045207,DRS025832,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing ES1 and EGFP,ES1 1,SAMD00044055,,sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044055,DRX045207,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044055,,,,584599765.0,3941083.0,DRR050165,0:148.33,A:164329030;C:129885620;G:136727379;T:153657736;N:0,148,,,,164329030,129885620,136727379,153657736,0,DRX045207,DRS025832,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.83769,,0.25395,,0.83116,,0.52784,,185,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
98,DRR050164,DRX045206,DRS025831,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 3,SAMD00044054,,sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044054,DRX045206,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044054,,,,343014114.0,3827762.0,DRR050164,0:89.61,A:99421434;C:73070267;G:77738821;T:92783592;N:0,89,,,,99421434,73070267,77738821,92783592,0,DRX045206,DRS025831,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.78953,,0.25529,,0.87367,,0.52148,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
99,DRR050163,DRX045205,DRS025830,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 2,SAMD00044053,,sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044053,DRX045205,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044053,,,,533069427.0,3824140.0,DRR050163,0:139.40,A:152608173;C:113928273;G:120051739;T:146481242;N:0,139,,,,152608173,113928273,120051739,146481242,0,DRX045205,DRS025830,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.80412,,0.26768,,0.85338,,0.52255,,245,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
100,DRR050162,DRX045204,DRS025829,DRP003043,PRJDB4416,Transcriptome analysis in ES1 expressing rods of zebrafish,DRP003043,Transcriptome Analysis,Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.,,,Zebrafish rods expressing EGFP,EGFP 1,SAMD00044052,,sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod,,,,,,,,,Ion Torrent PGM sequencing of SAMD00044052,DRX045204,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</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>,DRP003043,Ion Torrent PGM sequencing of SAMD00044052,,,,478262965.0,4224064.0,DRR050162,0:113.22,A:136348264;C:104872341;G:113114502;T:123927858;N:0,113,,,,136348264,104872341,113114502,123927858,0,DRX045204,DRS025829,DRA004229,"OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ.",Osaka university,1,0.86947,,0.29839,,0.83317,,0.51453,,80,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2016-03-09,Undetermined,Undetermined,Fin,Surface Structure
35557,SRR32880273,SRX28160884,SRS24513822,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema exercised exp bio rep 5,GSM8875053,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing,3dpa blastema exercised exp bio rep 5,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised,GSM8875053,GSM8875053: 3dpa blastema exercised exp bio rep 5; Danio rerio; RNA Seq,GSM8875053 r1,GSM8875053,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Exp_5_raw.fastq.gz,fastq,3833406286.0,31421363.0,GSM8875053 r1,0:122,A:1051289152;C:808410920;G:908646262;T:1064964960;N:94992,122,,,,1051289152,808410920,908646262,1064964960,94992,SRX28160884,SRS24513822,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35558,SRR32880274,SRX28160883,SRS24513821,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema exercised exp bio rep 4,GSM8875052,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing,3dpa blastema exercised exp bio rep 4,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised,GSM8875052,GSM8875052: 3dpa blastema exercised exp bio rep 4; Danio rerio; RNA Seq,GSM8875052 r1,GSM8875052,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Exp_4_raw.fastq.gz,fastq,2716320484.0,22264922.0,GSM8875052 r1,0:122,A:753716648;C:572683669;G:633777091;T:756074187;N:68889,122,,,,753716648,572683669,633777091,756074187,68889,SRX28160883,SRS24513821,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35559,SRR32880275,SRX28160882,SRS24513820,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema exercised exp bio rep 3,GSM8875051,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing,3dpa blastema exercised exp bio rep 3,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised,GSM8875051,GSM8875051: 3dpa blastema exercised exp bio rep 3; Danio rerio; RNA Seq,GSM8875051 r1,GSM8875051,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Exp_3_raw.fastq.gz,fastq,3326494944.0,27266352.0,GSM8875051 r1,0:122,A:929692130;C:705713811;G:773972336;T:917030832;N:85835,122,,,,929692130,705713811,773972336,917030832,85835,SRX28160882,SRS24513820,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35560,SRR32880276,SRX28160881,SRS24513819,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema exercised exp bio rep 2,GSM8875050,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing,3dpa blastema exercised exp bio rep 2,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised,GSM8875050,GSM8875050: 3dpa blastema exercised exp bio rep 2; Danio rerio; RNA Seq,GSM8875050 r1,GSM8875050,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Exp_2_raw.fastq.gz,fastq,3319809954.0,27211557.0,GSM8875050 r1,0:122,A:912008882;C:704589377;G:783108238;T:920018852;N:84605,122,,,,912008882,704589377,783108238,920018852,84605,SRX28160881,SRS24513819,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35561,SRR32880277,SRX28160880,SRS24513818,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema exercised exp bio rep 1,GSM8875049,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised|geo loc name:missing|collection date:missing,3dpa blastema exercised exp bio rep 1,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Swim exercised,GSM8875049,GSM8875049: 3dpa blastema exercised exp bio rep 1; Danio rerio; RNA Seq,GSM8875049 r1,GSM8875049,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Exp_1_raw.fastq.gz,fastq,3744436322.0,30692101.0,GSM8875049 r1,0:122,A:1050863937;C:775277972;G:866627322;T:1051571183;N:95908,122,,,,1050863937,775277972,866627322,1051571183,95908,SRX28160880,SRS24513818,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35562,SRR32880278,SRX28160879,SRS24513817,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema unexercised control bio rep 5,GSM8875048,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,3dpa blastema unexercised control bio rep 5,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control,GSM8875048,GSM8875048: 3dpa blastema unexercised control bio rep 5; Danio rerio; RNA Seq,GSM8875048 r1,GSM8875048,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Control_5_raw.fastq.gz,fastq,3076092628.0,25213874.0,GSM8875048 r1,0:122,A:850913805;C:643783202;G:725071885;T:856245838;N:77898,122,,,,850913805,643783202,725071885,856245838,77898,SRX28160879,SRS24513817,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35563,SRR32880279,SRX28160878,SRS24513816,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema unexercised control bio rep 4,GSM8875047,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,3dpa blastema unexercised control bio rep 4,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control,GSM8875047,GSM8875047: 3dpa blastema unexercised control bio rep 4; Danio rerio; RNA Seq,GSM8875047 r1,GSM8875047,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Control_4_raw.fastq.gz,fastq,3458014848.0,28344384.0,GSM8875047 r1,0:122,A:946385067;C:748704825;G:821787294;T:941050744;N:86918,122,,,,946385067,748704825,821787294,941050744,86918,SRX28160878,SRS24513816,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35564,SRR32880280,SRX28160877,SRS24513815,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema unexercised control bio rep 3,GSM8875046,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,3dpa blastema unexercised control bio rep 3,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control,GSM8875046,GSM8875046: 3dpa blastema unexercised control bio rep 3; Danio rerio; RNA Seq,GSM8875046 r1,GSM8875046,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Control_3_raw.fastq.gz,fastq,3750141896.0,30738868.0,GSM8875046 r1,0:122,A:1016915650;C:830734179;G:908080650;T:994316527;N:94890,122,,,,1016915650,830734179,908080650,994316527,94890,SRX28160877,SRS24513815,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35565,SRR32880281,SRX28160876,SRS24513814,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema unexercised control bio rep 2,GSM8875045,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,3dpa blastema unexercised control bio rep 2,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control,GSM8875045,GSM8875045: 3dpa blastema unexercised control bio rep 2; Danio rerio; RNA Seq,GSM8875045 r1,GSM8875045,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Control_2_raw.fastq.gz,fastq,3559797740.0,29178670.0,GSM8875045 r1,0:122,A:940502236;C:815297194;G:877321806;T:926584991;N:91513,122,,,,940502236,815297194,877321806,926584991,91513,SRX28160876,SRS24513814,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
35566,SRR32880282,SRX28160875,SRS24513812,SRP573530,PRJNA1242724,Early exercise disrupts a pro repair extracellular matrix program during zebrafish fin regeneration,GSE293062,Transcriptome Analysis,Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading  initiated before or during blastema formation  resulted in reduced regenerative outcomes. Long term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix ECM gene expression program  including for hyaluronic acid HA synthesis. Like exercise loading  HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury upregulated HA establishes a pro regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes associated protein Yap. Further  exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage dependent response similar to that seen in mammalian skeletal repair  where early exercise—applied during blastema establishment—impairs regeneration  while delayed loading during outgrowth does not  suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes. Overall design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise exp or unexercised controls control,,,,3dpa blastema unexercised control bio rep 1,GSM8875044,,source name:whole caudal fin 3 dpa blastema|tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,3dpa blastema unexercised control bio rep 1,Reads were aligned with Kallisto Pachter lab against zebrafish reference transcriptome. Assembly: GRCz11 Supplementary files format and content: .h5 counts abundance files,whole caudal fin 3 dpa blastema,Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,Zebrafish age 3 month 12 month were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily,tissue:whole caudal fin 3 dpa blastema|genotype:WT|treatment:Control,GSM8875044,GSM8875044: 3dpa blastema unexercised control bio rep 1; Danio rerio; RNA Seq,GSM8875044 r1,GSM8875044,1,RNA was prepared using a Direct Zol RNA prep kit Zymogenetics and eluted into water. RNA was pooled from 2 male and 2 female size matched fish for each replicate with replicates spanning two independent swimming cohorts. Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit  indexed and pooled  and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP573530,,,Control_1_raw.fastq.gz,fastq,3410581248.0,27955584.0,GSM8875044 r1,0:122,A:908666390;C:784237057;G:832115119;T:885476069;N:86613,122,,,,908666390,784237057,832115119,885476069,86613,SRX28160875,SRS24513812,SRA2100952,"Stankunas, Institute of Molecular Biology, University of Oregon","Stankunas, Institute of Molecular Biology, University of Oregon",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2025-03-27,Adult,Adult,Fin,Surface Structure
40134,SRR2834938,SRX1389532,SRS1136849,SRP065355,PRJNA300314,Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration,GSE74415,Transcriptome Analysis,Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors.  MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation  we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing.  The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.,,pubmed:27355827,,4dpa small RNA  rep 3,GSM1920160,,source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:small RNA,4dpa small RNA  rep 3,Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA  and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample.,caudal fin,Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222.,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.,tissue:caudal fin|dy post amputation:4|library type:small RNA,GSM1920160,GSM1920160: 4dpa small RNA  rep 3; Danio rerio; RNA Seq,GSM1920160,,1,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,GEO Accession:GSM1920160,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065355,,,RPD2-A3_ATGTCA_L007_R1_001.fastq.gz,fastq,373679650.0,7473593.0,GSM1920160 r1,0:50,A:68694509;C:89847229;G:118844938;T:95955229;N:337745,50,,,,68694509,89847229,118844938,95955229,337745,SRX1389532,SRS1136849,SRA307553,GEO,"Molecular and Biomedical Sciences, University of Maine",1,0.11965,,0.00285,,0.99433,,0.52581,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2015-10-27,Adult,Adult,Fin,Surface Structure
40135,SRR2834937,SRX1389531,SRS1136850,SRP065355,PRJNA300314,Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration,GSE74415,Transcriptome Analysis,Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors.  MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation  we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing.  The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.,,pubmed:27355827,,4dpa small RNA  rep 2,GSM1920159,,source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:small RNA,4dpa small RNA  rep 2,Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA  and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample.,caudal fin,Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222.,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.,tissue:caudal fin|dy post amputation:4|library type:small RNA,GSM1920159,GSM1920159: 4dpa small RNA  rep 2; Danio rerio; RNA Seq,GSM1920159,,1,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,GEO Accession:GSM1920159,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065355,,,RPD2-A2_AGTTCC_L007_R1_001.fastq.gz,fastq,445390000.0,8907800.0,GSM1920159 r1,0:50,A:81500522;C:106498774;G:142041440;T:114948557;N:400707,50,,,,81500522,106498774,142041440,114948557,400707,SRX1389531,SRS1136850,SRA307553,GEO,"Molecular and Biomedical Sciences, University of Maine",1,0.16246,,0.00439,,0.99506,,0.52311,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2015-10-27,Adult,Adult,Fin,Surface Structure
40136,SRR2834936,SRX1389530,SRS1136851,SRP065355,PRJNA300314,Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration,GSE74415,Transcriptome Analysis,Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors.  MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation  we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing.  The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.,,pubmed:27355827,,4dpa small RNA  rep 1,GSM1920158,,source name:caudal fin|tissue:caudal fin|dy post amputation:4|library type:small RNA,4dpa small RNA  rep 1,Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA  and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample.,caudal fin,Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222.,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.,tissue:caudal fin|dy post amputation:4|library type:small RNA,GSM1920158,GSM1920158: 4dpa small RNA  rep 1; Danio rerio; RNA Seq,GSM1920158,,1,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,GEO Accession:GSM1920158,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065355,,,RPD2-A1_AGTCAA_L007_R1_001.fastq.gz,fastq,447070900.0,8941418.0,GSM1920158 r1,0:50,A:81330845;C:108093874;G:142869603;T:114376524;N:400054,50,,,,81330845,108093874,142869603,114376524,400054,SRX1389530,SRS1136851,SRA307553,GEO,"Molecular and Biomedical Sciences, University of Maine",1,0.19014,,0.00382,,0.99484,,0.52592,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2015-10-27,Adult,Adult,Fin,Surface Structure
40137,SRR2834935,SRX1389529,SRS1136852,SRP065355,PRJNA300314,Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration,GSE74415,Transcriptome Analysis,Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors.  MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation  we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing.  The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.,,pubmed:27355827,,0dpa small RNA  rep 3,GSM1920157,,source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:small RNA,0dpa small RNA  rep 3,Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA  and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample.,caudal fin,Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222.,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.,tissue:caudal fin|dy post amputation:0|library type:small RNA,GSM1920157,GSM1920157: 0dpa small RNA  rep 3; Danio rerio; RNA Seq,GSM1920157,,1,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,GEO Accession:GSM1920157,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065355,,,UPD2-A3_GCCAAT_L007_R1_001.fastq.gz,fastq,262275650.0,5245513.0,GSM1920157 r1,0:50,A:50807514;C:65746360;G:82912384;T:62571646;N:237746,50,,,,50807514,65746360,82912384,62571646,237746,SRX1389529,SRS1136852,SRA307553,GEO,"Molecular and Biomedical Sciences, University of Maine",1,0.13825,,0.00592,,0.99401,,0.53009,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2015-10-27,Adult,Adult,Fin,Surface Structure
40138,SRR2834934,SRX1389528,SRS1136853,SRP065355,PRJNA300314,Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration,GSE74415,Transcriptome Analysis,Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors.  MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation  we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing.  The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.,,pubmed:27355827,,0dpa small RNA  rep 2,GSM1920156,,source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:small RNA,0dpa small RNA  rep 2,Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA  and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample.,caudal fin,Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222.,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.,tissue:caudal fin|dy post amputation:0|library type:small RNA,GSM1920156,GSM1920156: 0dpa small RNA  rep 2; Danio rerio; RNA Seq,GSM1920156,,1,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,GEO Accession:GSM1920156,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065355,,,UPD2-A2_ACAGTG_L007_R1_001.fastq.gz,fastq,754057150.0,15081143.0,GSM1920156 r1,0:50,A:136745812;C:183633004;G:238526597;T:194475603;N:676134,50,,,,136745812,183633004,238526597,194475603,676134,SRX1389528,SRS1136853,SRA307553,GEO,"Molecular and Biomedical Sciences, University of Maine",1,0.09694,,0.00492,,0.99381,,0.54425,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2015-10-27,Adult,Adult,Fin,Surface Structure
40139,SRR2834933,SRX1389527,SRS1136854,SRP065355,PRJNA300314,Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration,GSE74415,Transcriptome Analysis,Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors.  MicroRNAs are short highly conserved non coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation  we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing.  The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 dy post amputation.,,pubmed:27355827,,0dpa small RNA  rep 1,GSM1920155,,source name:caudal fin|tissue:caudal fin|dy post amputation:0|library type:small RNA,0dpa small RNA  rep 1,Reads were adapter clipped and quality filtered using FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/ for small RNA  and Trimmomatic Bolger et al. Bioinformatics 2010 for mRNA. Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner Wheeler et al. Evol. Dev. 2009 and miRBase v. 21 Kozomara et al. Nucleic Acids Res 2014. MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR Robinson et al. Bioinformatics 2010. mRNA reads were mapped to the zebrafish transcriptome Ensembl v. 76 annotation of zebrafish Zv9 assembly using RSEM Li and Dewey BMC Bioinformatics 2011. Differentially expressed transcripts were determined using R/edgeR. Genome build: zv9 Supplementary files format and content: Tab delimited text file with read counts per transcript per sample.,caudal fin,Caudal fins were amputated with scalpels following anesthesia 0.6mM MS222.,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,Adult Ekkwill EK zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.,tissue:caudal fin|dy post amputation:0|library type:small RNA,GSM1920155,GSM1920155: 0dpa small RNA  rep 1; Danio rerio; RNA Seq,GSM1920155,,1,Total RNA was isolated using TRI Reagent Molecular Research Center  Inc.  Cincinnati  OH following manufacturer’s protocol. Illumina TruSeq small RNA and strand specific PolyA+ mRNA libraries.,GEO Accession:GSM1920155,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065355,,,UPD2-A1_TGACCA_L007_R1_001.fastq.gz,fastq,617544950.0,12350899.0,GSM1920155 r1,0:50,A:112140176;C:151825965;G:197163658;T:155854533;N:560618,50,,,,112140176,151825965,197163658,155854533,560618,SRX1389527,SRS1136854,SRA307553,GEO,"Molecular and Biomedical Sciences, University of Maine",1,0.10954,,0.00515,,0.99295,,0.553,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2015-10-27,Adult,Adult,Fin,Surface Structure
40334,SRR3086895,SRX1518389,SRS1236744,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 2,GSM2028020,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028020,GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq,GSM2028020,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un2-1.fastq.gz,fastq,800000000.0,16000000.0,GSM2028020 r1,0:50,A:210926663;C:190496048;G:184518152;T:213985916;N:73221,50,,,,210926663,190496048,184518152,213985916,73221,SRX1518389,SRS1236744,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91126,,0.08857,,0.72054,,0.44807,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40335,SRR3086896,SRX1518389,SRS1236744,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 2,GSM2028020,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028020,GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq,GSM2028020,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un2-2.fastq.gz,fastq,800000000.0,16000000.0,GSM2028020 r2,0:50,A:210822728;C:190175530;G:185124231;T:213867287;N:10224,50,,,,210822728,190175530,185124231,213867287,10224,SRX1518389,SRS1236744,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.90559,,0.08872,,0.7194,,0.43319,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40336,SRR3086897,SRX1518389,SRS1236744,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 2,GSM2028020,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028020,GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq,GSM2028020,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un2-3.fastq.gz,fastq,46067800.0,921356.0,GSM2028020 r3,0:50,A:12182398;C:10879021;G:10673094;T:12333021;N:266,50,,,,12182398,10879021,10673094,12333021,266,SRX1518389,SRS1236744,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.89253,,0.08727,,0.72094,,0.45046,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40337,SRR3086892,SRX1518388,SRS1236746,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 1,GSM2028019,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028019,GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq,GSM2028019,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un1-1.fastq.gz,fastq,800000000.0,16000000.0,GSM2028019 r1,0:50,A:206270357;C:193369997;G:191677237;T:208652195;N:30214,50,,,,206270357,193369997,191677237,208652195,30214,SRX1518388,SRS1236746,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91334,,0.07414,,0.73034,,0.44343,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40338,SRR3086893,SRX1518388,SRS1236746,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 1,GSM2028019,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028019,GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq,GSM2028019,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un1-2.fastq.gz,fastq,493137350.0,9862747.0,GSM2028019 r2,0:50,A:127272457;C:119005858;G:118176094;T:128679179;N:3762,50,,,,127272457,119005858,118176094,128679179,3762,SRX1518388,SRS1236746,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.90901,,0.07418,,0.73085,,0.44107,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40339,SRR3086894,SRX1518388,SRS1236746,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF Uninjured Fin 1,GSM2028019,,tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1,ZF Uninjured Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Uninjured fins,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:N1,GSM2028019,GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq,GSM2028019,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Un1-3.fastq.gz,fastq,800000000.0,16000000.0,GSM2028019 r3,0:50,A:206410293;C:193573258;G:191140232;T:208806339;N:69878,50,,,,206410293,193573258,191140232,208806339,69878,SRX1518388,SRS1236746,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91744,,0.07298,,0.72847,,0.44383,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40340,SRR3086888,SRX1518387,SRS1236747,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 2,GSM2028018,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028018,GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq,GSM2028018,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg2-1.fastq.gz,fastq,800000000.0,16000000.0,GSM2028018 r1,0:50,A:208862526;C:192270727;G:188582591;T:210215639;N:68517,50,,,,208862526,192270727,188582591,210215639,68517,SRX1518387,SRS1236747,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.92514,,0.07091,,0.70638,,0.46239,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40341,SRR3086889,SRX1518387,SRS1236747,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 2,GSM2028018,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028018,GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq,GSM2028018,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg2-2.fastq.gz,fastq,800000000.0,16000000.0,GSM2028018 r2,0:50,A:208854177;C:192161932;G:188871135;T:210062448;N:50308,50,,,,208854177,192161932,188871135,210062448,50308,SRX1518387,SRS1236747,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.92252,,0.07056,,0.70694,,0.45392,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40342,SRR3086890,SRX1518387,SRS1236747,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 2,GSM2028018,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028018,GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq,GSM2028018,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg2-3.fastq.gz,fastq,800000000.0,16000000.0,GSM2028018 r3,0:50,A:208765699;C:191936198;G:189409194;T:209878960;N:9949,50,,,,208765699,191936198,189409194,209878960,9949,SRX1518387,SRS1236747,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91451,,0.06995,,0.70741,,0.45822,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40343,SRR3086891,SRX1518387,SRS1236747,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 2,GSM2028018,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 2,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028018,GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq,GSM2028018,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg2-4.fastq.gz,fastq,123651950.0,2473039.0,GSM2028018 r4,0:50,A:32365652;C:29515195;G:29236871;T:32533508;N:724,50,,,,32365652,29515195,29236871,32533508,724,SRX1518387,SRS1236747,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91437,,0.07079,,0.70867,,0.46558,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40344,SRR3086884,SRX1518386,SRS1236745,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 1,GSM2028017,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028017,GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq,GSM2028017,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg1-1.fastq.gz,fastq,800000000.0,16000000.0,GSM2028017 r1,0:50,A:207070768;C:193619920;G:189688453;T:209552804;N:68055,50,,,,207070768,193619920,189688453,209552804,68055,SRX1518386,SRS1236745,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.92944,,0.06242,,0.71224,,0.46274,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40345,SRR3086885,SRX1518386,SRS1236745,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 1,GSM2028017,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028017,GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq,GSM2028017,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg1-2.fastq.gz,fastq,800000000.0,16000000.0,GSM2028017 r2,0:50,A:207042635;C:193500947;G:190015843;T:209392450;N:48125,50,,,,207042635,193500947,190015843,209392450,48125,SRX1518386,SRS1236745,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.92402,,0.06138,,0.71295,,0.46332,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40346,SRR3086886,SRX1518386,SRS1236745,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 1,GSM2028017,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028017,GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq,GSM2028017,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg1-3.fastq.gz,fastq,800000000.0,16000000.0,GSM2028017 r3,0:50,A:206941368;C:193232860;G:190532195;T:209283728;N:9849,50,,,,206941368,193232860,190532195,209283728,9849,SRX1518386,SRS1236745,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91924,,0.06196,,0.71275,,0.46184,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
40347,SRR3086887,SRX1518386,SRS1236745,SRP068114,PRJNA307985,Transcription profiling of zebrafish fin regeneration,GSE76564,Transcriptome Analysis,We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins,,pubmed:27049946,,ZF 4dpa Fin 1,GSM2028017,,tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation,ZF 4dpa Fin 1,"Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: ""Regenerate fin counts.txt"" and ""Uninjured fin Control counts.txt"" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.",Fins 4d post amputation,Fins were amputated to 50% of their original length using razor blades,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,,strain:EK|line:Wild type|treatment:Fin Amputation,GSM2028017,GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq,GSM2028017,,1,Either uninjured fins or fins at 4 dy post amputation were collected.  10 fins were dissected  rinsed in PBS  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries,GEO Accession:GSM2028017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP068114,,,Reg1-4.fastq.gz,fastq,90897750.0,1817955.0,GSM2028017 r4,0:50,A:23579811;C:21833091;G:21640955;T:23843357;N:536,50,,,,23579811,21833091,21640955,23843357,536,SRX1518386,SRS1236745,SRA329570,GEO,"Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center",1,0.91241,,0.06085,,0.7152,,0.46013,,50,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,unknown,bulk,unknown,unknown,,United States,2016-01-05,Undetermined,Undetermined,Fin,Surface Structure
48021,SRR6915090,SRX3862779,SRS3104834,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,10dpa replicate3,GSM3071386,,source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,10dpa replicate3,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 10 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071386,GSM3071386: 10dpa replicate3; Danio rerio; RNA Seq,GSM3071386,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071386,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L03-1-Idx_10-10.bam,bam,682375516.0,14088728.0,GSM3071386 r1,0:48.43,A:140419665;C:148759068;G:176799261;T:168695522;N:47702000,48,,,,140419665,148759068,176799261,168695522,47702000,SRX3862779,SRS3104834,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.76603,,0.04459,,0.79752,,0.50424,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48022,SRR6915089,SRX3862778,SRS3104833,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,3dpa replicate3,GSM3071385,,source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,3dpa replicate3,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 3 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071385,GSM3071385: 3dpa replicate3; Danio rerio; RNA Seq,GSM3071385,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071385,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L03-1-Idx_12-12.bam,bam,901887293.0,18522789.0,GSM3071385 r1,0:48.69,A:184300673;C:193849264;G:243428119;T:224471972;N:55837265,48,,,,184300673,193849264,243428119,224471972,55837265,SRX3862778,SRS3104833,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.78632,,0.03154,,0.79707,,0.51779,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48023,SRR6915088,SRX3862777,SRS3104832,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,2dpa replicate3,GSM3071384,,source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,2dpa replicate3,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 2 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071384,GSM3071384: 2dpa replicate3; Danio rerio; RNA Seq,GSM3071384,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071384,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L03-1-Idx_11-11.bam,bam,850810410.0,17462158.0,GSM3071384 r1,0:48.72,A:176186499;C:182052044;G:228063922;T:213571294;N:50936651,48,,,,176186499,182052044,228063922,213571294,50936651,SRX3862777,SRS3104832,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.77804,,0.03462,,0.80229,,0.49822,,43,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48024,SRR6915087,SRX3862776,SRS3104831,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,0dpa replicate3,GSM3071383,,source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,0dpa replicate3,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 0 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071383,GSM3071383: 0dpa replicate3; Danio rerio; RNA Seq,GSM3071383,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071383,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L03-1-Idx_9-9.bam,bam,598710241.0,12328728.0,GSM3071383 r1,0:48.56,A:121889198;C:129444719;G:158430979;T:150128070;N:38817275,48,,,,121889198,129444719,158430979,150128070,38817275,SRX3862776,SRS3104831,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.77,,0.03334,,0.799,,0.45925,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48025,SRR6915086,SRX3862775,SRS3104830,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,10dpa replicate2,GSM3071382,,source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,10dpa replicate2,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 10 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071382,GSM3071382: 10dpa replicate2; Danio rerio; RNA Seq,GSM3071382,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071382,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L02-1-Idx_8-8.bam,bam,1205021238.0,24639106.0,GSM3071382 r1,0:48.91,A:255022070;C:275793907;G:309172527;T:294800027;N:70232707,48,,,,255022070,275793907,309172527,294800027,70232707,SRX3862775,SRS3104830,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.80398,,0.05829,,0.78644,,0.4993,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48026,SRR6915085,SRX3862774,SRS3104829,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,3dpa replicate2,GSM3071381,,source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,3dpa replicate2,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 3 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071381,GSM3071381: 3dpa replicate2; Danio rerio; RNA Seq,GSM3071381,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071381,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L02-1-Idx_10-10.bam,bam,1479531813.0,30219937.0,GSM3071381 r1,0:48.96,A:314793261;C:331769330;G:384109921;T:369987947;N:78871354,48,,,,314793261,331769330,384109921,369987947,78871354,SRX3862774,SRS3104829,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.81777,,0.03195,,0.7821,,0.49263,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48027,SRR6915084,SRX3862773,SRS3104828,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,2dpa replicate2,GSM3071380,,source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,2dpa replicate2,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 2 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071380,GSM3071380: 2dpa replicate2; Danio rerio; RNA Seq,GSM3071380,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071380,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L02-1-Idx_9-9.bam,bam,834856811.0,17079585.0,GSM3071380 r1,0:48.88,A:179851654;C:186667201;G:209784080;T:212166083;N:46387793,48,,,,179851654,186667201,209784080,212166083,46387793,SRX3862773,SRS3104828,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.80341,,0.02786,,0.78031,,0.49876,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48028,SRR6915083,SRX3862772,SRS3104827,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,0dpa replicate2,GSM3071379,,source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,0dpa replicate2,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 0 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071379,GSM3071379: 0dpa replicate2; Danio rerio; RNA Seq,GSM3071379,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071379,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L02-1-Idx_7-7.bam,bam,821645371.0,16824250.0,GSM3071379 r1,0:48.84,A:169383232;C:176200663;G:223364159;T:207905438;N:44791879,48,,,,169383232,176200663,223364159,207905438,44791879,SRX3862772,SRS3104827,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.79697,,0.04152,,0.79513,,0.48078,,34,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48029,SRR6915082,SRX3862771,SRS3104826,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,10dpa replicate1,GSM3071378,,source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,10dpa replicate1,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 10 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071378,GSM3071378: 10dpa replicate1; Danio rerio; RNA Seq,GSM3071378,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071378,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L01-1-Idx_4-4.bam,bam,1056921416.0,21553661.0,GSM3071378 r1,0:49.04,A:223138065;C:233998717;G:286278215;T:261736901;N:51769518,49,,,,223138065,233998717,286278215,261736901,51769518,SRX3862771,SRS3104826,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.81372,,0.06015,,0.79017,,0.49818,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48030,SRR6915081,SRX3862770,SRS3104824,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,3dpa replicate1,GSM3071377,,source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,3dpa replicate1,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 3 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071377,GSM3071377: 3dpa replicate1; Danio rerio; RNA Seq,GSM3071377,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071377,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L01-1-Idx_6-6.bam,bam,614372216.0,12531168.0,GSM3071377 r1,0:49.03,A:129828689;C:133826356;G:168985348;T:153858339;N:27873484,49,,,,129828689,133826356,168985348,153858339,27873484,SRX3862770,SRS3104824,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.81659,,0.02803,,0.78987,,0.49295,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48031,SRR6915080,SRX3862769,SRS3104825,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,2dpa replicate1,GSM3071376,,source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,2dpa replicate1,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 2 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071376,GSM3071376: 2dpa replicate1; Danio rerio; RNA Seq,GSM3071376,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071376,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L01-1-Idx_5-5.bam,bam,1317408760.0,26870813.0,GSM3071376 r1,0:49.03,A:278980295;C:285236037;G:357022664;T:334390621;N:61779143,49,,,,278980295,285236037,357022664,334390621,61779143,SRX3862769,SRS3104825,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.81546,,0.02559,,0.79328,,0.48857,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48032,SRR6915079,SRX3862768,SRS3104823,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,0dpa replicate1,GSM3071375,,source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,0dpa replicate1,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 0 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071375,GSM3071375: 0dpa replicate1; Danio rerio; RNA Seq,GSM3071375,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071375,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L01-1-Idx_3-3.bam,bam,975324708.0,19881338.0,GSM3071375 r1,0:49.06,A:203549346;C:215407985;G:265949502;T:244027187;N:46390688,49,,,,203549346,215407985,265949502,244027187,46390688,SRX3862768,SRS3104823,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.80817,,0.05047,,0.79569,,0.47149,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
51072,SRR8503426,SRX5307303,SRS4304843,SRP182846,PRJNA517717,Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration,GSE125859,Transcriptome Analysis,"Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing ""niche"" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue  as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.",,,,prox 4,GSM3583370,,source name:96 hpa proximal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,prox 4,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa proximal regenerate,,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM3583370,GSM3583370: prox 4; Danio rerio; RNA Seq,GSM3583370,,1,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM3583370,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP182846,,,P_H4_S10_R1_001.fastq,fastq,2542575470.0,30622171.0,GSM3583370 r1,0:83.03 1:0,A:589076767;C:639351667;G:597170951;T:716352530;N:623555,83,0,,,589076767,639351667,597170951,716352530,623555,SRX5307303,SRS4304843,SRA841050,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.96003,,0.11536,,0.73184,,0.50861,,82,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-29,Undetermined,Undetermined,Fin,Surface Structure
51073,SRR8503425,SRX5307302,SRS4304842,SRP182846,PRJNA517717,Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration,GSE125859,Transcriptome Analysis,"Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing ""niche"" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue  as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.",,,,prox 3,GSM3583369,,source name:96 hpa proximal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,prox 3,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa proximal regenerate,,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM3583369,GSM3583369: prox 3; Danio rerio; RNA Seq,GSM3583369,,1,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM3583369,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP182846,,,P_H3_S6_R1_001.fastq,fastq,2572355378.0,30989968.0,GSM3583369 r1,0:83.01 1:0,A:628074006;C:625169881;G:585755261;T:732650748;N:705482,83,0,,,628074006,625169881,585755261,732650748,705482,SRX5307302,SRS4304842,SRA841050,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.95739,,0.12653,,0.72066,,0.49327,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-29,Undetermined,Undetermined,Fin,Surface Structure
51074,SRR8503424,SRX5307301,SRS4304841,SRP182846,PRJNA517717,Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration,GSE125859,Transcriptome Analysis,"Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing ""niche"" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue  as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.",,,,prox 2,GSM3583368,,source name:96 hpa proximal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,prox 2,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa proximal regenerate,,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM3583368,GSM3583368: prox 2; Danio rerio; RNA Seq,GSM3583368,,1,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM3583368,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP182846,,,P_H2_S2_R1_001.fastq,fastq,2715018138.0,32683271.0,GSM3583368 r1,0:83.07 1:0,A:650816207;C:672048834;G:625641446;T:765832919;N:678732,83,0,,,650816207,672048834,625641446,765832919,678732,SRX5307301,SRS4304841,SRA841050,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.96137,,0.11136,,0.72299,,0.49133,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-29,Undetermined,Undetermined,Fin,Surface Structure
51075,SRR8503423,SRX5307300,SRS4304840,SRP182846,PRJNA517717,Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration,GSE125859,Transcriptome Analysis,"Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing ""niche"" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue  as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.",,,,dist 4,GSM3583367,,source name:96 hpa distal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,dist 4,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa distal regenerate,,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM3583367,GSM3583367: dist 4; Danio rerio; RNA Seq,GSM3583367,,1,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM3583367,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP182846,,,D_H4_S9_R1_001.fastq,fastq,2464857182.0,29674986.0,GSM3583367 r1,0:83.06 1:0,A:605468091;C:597283347;G:564251292;T:696611465;N:1242987,83,0,,,605468091,597283347,564251292,696611465,1242987,SRX5307300,SRS4304840,SRA841050,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.95564,,0.13712,,0.72492,,0.52324,,83,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-29,Undetermined,Undetermined,Fin,Surface Structure
51076,SRR8503422,SRX5307299,SRS4304839,SRP182846,PRJNA517717,Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration,GSE125859,Transcriptome Analysis,"Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing ""niche"" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue  as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.",,,,dist 3,GSM3583366,,source name:96 hpa distal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,dist 3,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa distal regenerate,,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM3583366,GSM3583366: dist 3; Danio rerio; RNA Seq,GSM3583366,,1,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM3583366,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP182846,,,D_H3_S5_R1_001.fastq,fastq,2722788315.0,32775698.0,GSM3583366 r1,0:83.07 1:0,A:668412932;C:661166177;G:622685501;T:770010239;N:513466,83,0,,,668412932,661166177,622685501,770010239,513466,SRX5307299,SRS4304839,SRA841050,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.95609,,0.14248,,0.71855,,0.51164,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-29,Undetermined,Undetermined,Fin,Surface Structure
51077,SRR8503421,SRX5307298,SRS4304838,SRP182846,PRJNA517717,Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration,GSE125859,Transcriptome Analysis,"Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing ""niche"" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue  as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.",,,,dist 2,GSM3583365,,source name:96 hpa distal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,dist 2,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa distal regenerate,,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM3583365,GSM3583365: dist 2; Danio rerio; RNA Seq,GSM3583365,,1,Tissue was collected and immediately placed in TRIzol reagent  and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM3583365,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP182846,,,D_H2_S1_R1_001.fastq,fastq,2701672782.0,32524371.0,GSM3583365 r1,0:83.07 1:0,A:655498678;C:666854715;G:624383445;T:753418035;N:1517909,83,0,,,655498678,666854715,624383445,753418035,1517909,SRX5307298,SRS4304838,SRA841050,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.95937,,0.14803,,0.72569,,0.5327,,81,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-29,Undetermined,Undetermined,Fin,Surface Structure
54194,SRR10106419,SRX6838311,SRS5379334,SRP221490,PRJNA565225,longfin causes cis ectopic expression of the kcnh2a ether a go go K+ channel to autonomously prolong fin outgrowth,GSE137352,Transcriptome Analysis,longfin mutant zebrafish grow and regenerate abnormally long fins. We sought to determine misregulated transcripts in the distal regenerate of 96 hpa caudal fins that could contribute to fin overgrowth or be the longfin causal gene. Overall design: We used RNA Seq to compare gene expression between replicates of microdissected distal regenerating fin tissue  distinguished by GFP negative tissue distal to sp7:GFP expressing cells  collected from longfin heterozygous adult fish and homozygous wildtype clutchmates. Each replicate consisted of pooled tissue from four caudal fins.,,,,WT 2,GSM4076982,,source name:96 hpa WT distal regenerate|genotype:wildtype|transgene:sp7:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,WT 2,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa WT distal regenerate,,Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction. Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,genotype:wildtype|transgene:sp7:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM4076982,GSM4076982: WT 2; Danio rerio; RNA Seq,GSM4076982,,1,Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction. Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM4076982,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221490,,,WT_2_S11_L001_R1_001.fastq,fastq,3503248731.0,34685631.0,GSM4076982 r1,0:101 1:0,A:856635056;C:863594849;G:805408294;T:977416095;N:194437,101,0,,,856635056,863594849,805408294,977416095,194437,SRX6838311,SRS5379334,SRA961168,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.94631,,0.13289,,0.71407,,0.50936,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-09-12,Undetermined,Adult,Fin,Surface Structure
54195,SRR10106418,SRX6838310,SRS5379333,SRP221490,PRJNA565225,longfin causes cis ectopic expression of the kcnh2a ether a go go K+ channel to autonomously prolong fin outgrowth,GSE137352,Transcriptome Analysis,longfin mutant zebrafish grow and regenerate abnormally long fins. We sought to determine misregulated transcripts in the distal regenerate of 96 hpa caudal fins that could contribute to fin overgrowth or be the longfin causal gene. Overall design: We used RNA Seq to compare gene expression between replicates of microdissected distal regenerating fin tissue  distinguished by GFP negative tissue distal to sp7:GFP expressing cells  collected from longfin heterozygous adult fish and homozygous wildtype clutchmates. Each replicate consisted of pooled tissue from four caudal fins.,,,,WT 1,GSM4076981,,source name:96 hpa WT distal regenerate|genotype:wildtype|transgene:sp7:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,WT 1,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa WT distal regenerate,,Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction. Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,genotype:wildtype|transgene:sp7:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM4076981,GSM4076981: WT 1; Danio rerio; RNA Seq,GSM4076981,,1,Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction. Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM4076981,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221490,,,WT_1_S10_L001_R1_001.fastq,fastq,3199705452.0,31680252.0,GSM4076981 r1,0:101 1:0,A:778841443;C:803844530;G:739237022;T:877613128;N:169329,101,0,,,778841443,803844530,739237022,877613128,169329,SRX6838310,SRS5379333,SRA961168,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.94697,,0.15905,,0.72707,,0.53718,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-09-12,Undetermined,Adult,Fin,Surface Structure
54196,SRR10106417,SRX6838309,SRS5379332,SRP221490,PRJNA565225,longfin causes cis ectopic expression of the kcnh2a ether a go go K+ channel to autonomously prolong fin outgrowth,GSE137352,Transcriptome Analysis,longfin mutant zebrafish grow and regenerate abnormally long fins. We sought to determine misregulated transcripts in the distal regenerate of 96 hpa caudal fins that could contribute to fin overgrowth or be the longfin causal gene. Overall design: We used RNA Seq to compare gene expression between replicates of microdissected distal regenerating fin tissue  distinguished by GFP negative tissue distal to sp7:GFP expressing cells  collected from longfin heterozygous adult fish and homozygous wildtype clutchmates. Each replicate consisted of pooled tissue from four caudal fins.,,,,lof 2,GSM4076980,,source name:96 hpa lof distal regenerate|genotype:longfin heterozygous|transgene:sp7:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,lof 2,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa lof distal regenerate,,Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction. Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,genotype:longfin heterozygous|transgene:sp7:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM4076980,GSM4076980: lof 2; Danio rerio; RNA Seq,GSM4076980,,1,Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction. Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM4076980,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221490,,,1_of_2_S8_L001_R1_001.fastq,fastq,2946970526.0,29177926.0,GSM4076980 r1,0:101 1:0,A:707921237;C:746733959;G:690249641;T:801925953;N:139736,101,0,,,707921237,746733959,690249641,801925953,139736,SRX6838309,SRS5379332,SRA961168,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.94681,,0.1304,,0.72261,,0.5216,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-09-12,Undetermined,Adult,Fin,Surface Structure
54197,SRR10106416,SRX6838308,SRS5379331,SRP221490,PRJNA565225,longfin causes cis ectopic expression of the kcnh2a ether a go go K+ channel to autonomously prolong fin outgrowth,GSE137352,Transcriptome Analysis,longfin mutant zebrafish grow and regenerate abnormally long fins. We sought to determine misregulated transcripts in the distal regenerate of 96 hpa caudal fins that could contribute to fin overgrowth or be the longfin causal gene. Overall design: We used RNA Seq to compare gene expression between replicates of microdissected distal regenerating fin tissue  distinguished by GFP negative tissue distal to sp7:GFP expressing cells  collected from longfin heterozygous adult fish and homozygous wildtype clutchmates. Each replicate consisted of pooled tissue from four caudal fins.,,,,lof 1,GSM4076979,,source name:96 hpa lof distal regenerate|genotype:longfin heterozygous|transgene:sp7:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,lof 1,Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided,96 hpa lof distal regenerate,,Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction. Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,,genotype:longfin heterozygous|transgene:sp7:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation,GSM4076979,GSM4076979: lof 1; Danio rerio; RNA Seq,GSM4076979,,1,Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction. Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA Seq kit and protocol.,GEO Accession:GSM4076979,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221490,,,1_of_1_S7_L001_R1_001.fastq,fastq,3227655081.0,31956981.0,GSM4076979 r1,0:101 1:0,A:797302923;C:790047797;G:741073759;T:899054640;N:175962,101,0,,,797302923,790047797,741073759,899054640,175962,SRX6838308,SRS5379331,SRA961168,GEO,"Stankunas, Biology- Institute of Molecular Biology, University of Oregon",1,0.94695,,0.12773,,0.71656,,0.51165,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-09-12,Undetermined,Adult,Fin,Surface Structure
58389,SRR11486781,SRX8062812,SRS6431234,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1,GSM4455083,,source name:whole fin|date:2 dpa|tissue:whole fin,RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,whole fin,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,date:2 dpa|tissue:whole fin,GSM4455083,GSM4455083: RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq,GSM4455083,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,GEO Accession:GSM4455083,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,JK-S8_S75_L008_R1_001.fastq.gz,fastq,2464411341.0,48321791.0,GSM4455083 r1,0:51 1:0,A:620643336;C:590840801;G:549905028;T:702758180;N:263996,51,0,,,620643336,590840801,549905028,702758180,263996,SRX8062812,SRS6431234,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91677,,0.09917,,0.71981,,0.46761,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-06,Multi-stage,Multi-stage,Fin,Surface Structure
58390,SRR11486780,SRX8062811,SRS6431233,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 2dpa; injured; batch 3; rep1,GSM4455082,,source name:whole fin|date:2 dpa|tissue:whole fin,RNAseq; whole fin; 2dpa; injured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,whole fin,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,date:2 dpa|tissue:whole fin,GSM4455082,GSM4455082: RNAseq; whole fin; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq,GSM4455082,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,GEO Accession:GSM4455082,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,JK-S6_S73_L008_R1_001.fastq.gz,fastq,2567417214.0,50341514.0,GSM4455082 r1,0:51 1:0,A:648888081;C:617286062;G:571907197;T:729086777;N:249097,51,0,,,648888081,617286062,571907197,729086777,249097,SRX8062811,SRS6431233,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91819,,0.10483,,0.72062,,0.45077,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-06,Multi-stage,Multi-stage,Fin,Surface Structure
58391,SRR11486779,SRX8062810,SRS6431232,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1,GSM4455081,,source name:whole fin|date:0 dpa|tissue:whole fin,RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,whole fin,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,date:0 dpa|tissue:whole fin,GSM4455081,GSM4455081: RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq,GSM4455081,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,GEO Accession:GSM4455081,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,JK-S7_S74_L008_R1_001.fastq.gz,fastq,2644840467.0,51859617.0,GSM4455081 r1,0:51 1:0,A:676588053;C:621109147;G:581574642;T:765307978;N:260647,51,0,,,676588053,621109147,581574642,765307978,260647,SRX8062810,SRS6431232,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.89598,,0.1281,,0.71417,,0.47147,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-06,Multi-stage,Multi-stage,Fin,Surface Structure
58392,SRR11486778,SRX8062809,SRS6431231,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1,GSM4455080,,source name:whole fin|date:0 dpa|tissue:whole fin,RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,whole fin,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,date:0 dpa|tissue:whole fin,GSM4455080,GSM4455080: RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq,GSM4455080,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,GEO Accession:GSM4455080,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,JK-S5_S72_L008_R1_001.fastq.gz,fastq,2412481254.0,47303554.0,GSM4455080 r1,0:51 1:0,A:616219239;C:570826024;G:531833820;T:693353914;N:248257,51,0,,,616219239,570826024,531833820,693353914,248257,SRX8062809,SRS6431231,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.90059,,0.11572,,0.72013,,0.46152,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-06,Multi-stage,Multi-stage,Fin,Surface Structure
58393,SRR11305419,SRX7910559,SRS6318068,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2,GSM4411419,,source name:RNAseq; Fibroblast; 4dpi; injured|time:4 dpa|tissue:fibroblast|genotype:wild type,RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; Fibroblast; 4dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:4 dpa|tissue:fibroblast|genotype:wild type,GSM4411419,GSM4411419: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2; Danio rerio; RNA Seq,GSM4411419,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411419,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,Fibro.RNAseq_injured_Regen_B2_S60_L008_R1_001.fastq.gz,fastq,3284939427.0,64410577.0,GSM4411419 r1,0:51 1:0,A:903305689;C:745606629;G:745227959;T:890156683;N:642467,51,0,,,903305689,745606629,745227959,890156683,642467,SRX7910559,SRS6318068,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.92145,,0.11147,,0.75091,,0.47874,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58394,SRR11305418,SRX7910558,SRS6318067,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1,GSM4411418,,source name:RNAseq; Fibroblast; 4dpi; injured|time:4 dpa|tissue:fibroblast|genotype:wild type,RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; Fibroblast; 4dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:4 dpa|tissue:fibroblast|genotype:wild type,GSM4411418,GSM4411418: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1; Danio rerio; RNA Seq,GSM4411418,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411418,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,Fibro.RNAseq_injured_Regen_A2_S59_L008_R1_001.fastq.gz,fastq,3208227063.0,62906413.0,GSM4411418 r1,0:51 1:0,A:889970085;C:720088600;G:719685444;T:877865381;N:617553,51,0,,,889970085,720088600,719685444,877865381,617553,SRX7910558,SRS6318067,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91814,,0.12108,,0.74704,,0.51875,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58395,SRR11305417,SRX7910557,SRS6318066,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2,GSM4411417,,source name:RNAseq; Fibroblast; 0dpi; uninjured|time:0 dpa|tissue:fibroblast|genotype:wild type,RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; Fibroblast; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:fibroblast|genotype:wild type,GSM4411417,GSM4411417: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2; Danio rerio; RNA Seq,GSM4411417,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411417,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,Fibro.RNAseq_uninjured_Uninj_B2_S58_L008_R1_001.fastq.gz,fastq,3779977251.0,74117201.0,GSM4411417 r1,0:51 1:0,A:1036587583;C:863955138;G:859693317;T:1019029136;N:712077,51,0,,,1036587583,863955138,859693317,1019029136,712077,SRX7910557,SRS6318066,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91762,,0.12285,,0.7683,,0.47877,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58396,SRR11305416,SRX7910556,SRS6318065,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1,GSM4411416,,source name:RNAseq; Fibroblast; 0dpi; uninjured|time:0 dpa|tissue:fibroblast|genotype:wild type,RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; Fibroblast; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:fibroblast|genotype:wild type,GSM4411416,GSM4411416: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq,GSM4411416,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411416,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,Fibro.RNAseq_uninjured_Uninj_A2_S57_L008_R1_001.fastq.gz,fastq,3830264271.0,75103221.0,GSM4411416 r1,0:51 1:0,A:1040171853;C:881400891;G:878214685;T:1029746894;N:729948,51,0,,,1040171853,881400891,878214685,1029746894,729948,SRX7910556,SRS6318065,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.92032,,0.09358,,0.75771,,0.4712,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58397,SRR11305415,SRX7910555,SRS6318064,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 1dpa; injured; batch 2; rep3,GSM4411415,,source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 1dpa; injured; batch 2; rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 1dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:1 dpa|tissue:whole fin|genotype:wild type,GSM4411415,GSM4411415: RNAseq; whole fin; 1dpa; injured; batch 2; rep3; Danio rerio; RNA Seq,GSM4411415,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411415,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_injured_RNA_1dpa_A_S37_L004_R1_001.fastq.gz,fastq,2924051085.0,57334335.0,GSM4411415 r1,0:51 1:0,A:678403251;C:734140605;G:692166374;T:819274692;N:66163,51,0,,,678403251,734140605,692166374,819274692,66163,SRX7910555,SRS6318064,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.93427,,0.06589,,0.73866,,0.45737,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58398,SRR11305414,SRX7910554,SRS6318063,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 1dpa; injured; batch 2; rep2,GSM4411414,,source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 1dpa; injured; batch 2; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 1dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:1 dpa|tissue:whole fin|genotype:wild type,GSM4411414,GSM4411414: RNAseq; whole fin; 1dpa; injured; batch 2; rep2; Danio rerio; RNA Seq,GSM4411414,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411414,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_injured_RNA_1dpa_B_S38_L004_R1_001.fastq.gz,fastq,3159176895.0,61944645.0,GSM4411414 r1,0:51 1:0,A:730026525;C:803379127;G:747179794;T:878521357;N:70092,51,0,,,730026525,803379127,747179794,878521357,70092,SRX7910554,SRS6318063,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.93516,,0.07492,,0.74602,,0.46646,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58399,SRR11305413,SRX7910553,SRS6318062,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 1dpa; injured; batch 2; rep1,GSM4411413,,source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 1dpa; injured; batch 2; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 1dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:1 dpa|tissue:whole fin|genotype:wild type,GSM4411413,GSM4411413: RNAseq; whole fin; 1dpa; injured; batch 2; rep1; Danio rerio; RNA Seq,GSM4411413,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411413,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_injured_RNA_1dpa_C_S39_L004_R1_001.fastq.gz,fastq,3053752296.0,59877496.0,GSM4411413 r1,0:51 1:0,A:705251373;C:775521263;G:724421121;T:848486693;N:71846,51,0,,,705251373,775521263,724421121,848486693,71846,SRX7910553,SRS6318062,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.9345,,0.08171,,0.74326,,0.47043,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58400,SRR11305412,SRX7910552,SRS6318061,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3,GSM4411412,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411412,GSM4411412: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3; Danio rerio; RNA Seq,GSM4411412,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411412,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_uninjured_RNA_0dpa_B_S35_L004_R1_001.fastq.gz,fastq,3095170620.0,60689620.0,GSM4411412 r1,0:51 1:0,A:728515579;C:769711604;G:717419279;T:879450837;N:73321,51,0,,,728515579,769711604,717419279,879450837,73321,SRX7910552,SRS6318061,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91314,,0.09911,,0.72498,,0.46006,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58401,SRR11305411,SRX7910551,SRS6318060,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2,GSM4411411,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411411,GSM4411411: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2; Danio rerio; RNA Seq,GSM4411411,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411411,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_uninjured_RNA_0dpa_C_S36_L004_R1_001.fastq.gz,fastq,2959811163.0,58035513.0,GSM4411411 r1,0:51 1:0,A:702000960;C:731163416;G:687625038;T:838953116;N:68633,51,0,,,702000960,731163416,687625038,838953116,68633,SRX7910551,SRS6318060,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91317,,0.09909,,0.7237,,0.45771,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58402,SRR11305410,SRX7910550,SRS6318059,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1,GSM4411410,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411410,GSM4411410: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1; Danio rerio; RNA Seq,GSM4411410,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411410,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_uninjured_RNA_0dpa_A_S34_L004_R1_001.fastq.gz,fastq,2850762963.0,55897313.0,GSM4411410 r1,0:51 1:0,A:675289993;C:707558547;G:662291002;T:805558844;N:64577,51,0,,,675289993,707558547,662291002,805558844,64577,SRX7910550,SRS6318059,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91288,,0.10801,,0.72165,,0.46866,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58403,SRR11305409,SRX7910549,SRS6318058,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 4dpa; injured; batch 1; rep2,GSM4411409,,source name:RNAseq; whole fin; 4dpi; injured|time:4 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 4dpa; injured; batch 1; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 4dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:4 dpa|tissue:whole fin|genotype:wild type,GSM4411409,GSM4411409: RNAseq; whole fin; 4dpa; injured; batch 1; rep2; Danio rerio; RNA Seq,GSM4411409,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411409,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin.RNAseq_injured_reg2.fastq.gz,fastq,2523651950.0,50473039.0,GSM4411409 r1,0:50,A:658848054;C:605884052;G:596099791;T:662690555;N:129498,50,,,,658848054,605884052,596099791,662690555,129498,SRX7910549,SRS6318058,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91959,,0.07092,,0.70717,,0.45829,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58404,SRR11305408,SRX7910548,SRS6318057,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 4dpa; injured; batch 1; rep1,GSM4411408,,source name:RNAseq; whole fin; 4dpi; injured|time:4 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 4dpa; injured; batch 1; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 4dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:4 dpa|tissue:whole fin|genotype:wild type,GSM4411408,GSM4411408: RNAseq; whole fin; 4dpa; injured; batch 1; rep1; Danio rerio; RNA Seq,GSM4411408,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411408,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin.RNAseq_injured_reg1.fastq.gz,fastq,2490897750.0,49817955.0,GSM4411408 r1,0:50,A:644634582;C:602186818;G:591877446;T:652072339;N:126565,50,,,,644634582,602186818,591877446,652072339,126565,SRX7910548,SRS6318057,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.92355,,0.06175,,0.71342,,0.46396,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58405,SRR11305407,SRX7910547,SRS6318056,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2,GSM4411407,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411407,GSM4411407: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2; Danio rerio; RNA Seq,GSM4411407,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411407,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin.RNAseq_uninjured_Uni2.fastq.gz,fastq,1646067800.0,32921356.0,GSM4411407 r1,0:50,A:433931789;C:391550599;G:380315477;T:440186224;N:83711,50,,,,433931789,391550599,380315477,440186224,83711,SRX7910547,SRS6318056,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.90771,,0.08897,,0.71985,,0.44509,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58406,SRR11305406,SRX7910546,SRS6318055,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1,GSM4411406,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411406,GSM4411406: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1; Danio rerio; RNA Seq,GSM4411406,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411406,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin.RNAseq_uninjured_Uni1.fastq.gz,fastq,2093137350.0,41862747.0,GSM4411406 r1,0:50,A:539953107;C:505949113;G:500993563;T:546137713;N:103854,50,,,,539953107,505949113,500993563,546137713,103854,SRX7910546,SRS6318055,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.9119,,0.07318,,0.72969,,0.43282,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
61953,SRR13075149,SRX9522192,SRS7729391,SRP292933,PRJNA679002,Role of Il 11 signaling in adult heart and fin regeneration in zebrafish,GSE161647,Transcriptome Analysis,In adult mammals  tissue damage post myocardial infarction induces myofibroblast differentiation and the formation of a permanent  functionally inert scar.  However  the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood.  Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis post tissue damage  including in the heart.  Here  employing comparative expression profiling coupled with loss of function approaches  we identified the canonical Interleukin 11/Stat3 signaling axis as a core component of regeneration in zebrafish.  Notably  animals with loss of Interleukin 11 receptor Il11ra function reach maturity without xxx developmental defects  but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar  similar to what is observed in adult mammals.  Using zebrafish fate mapping approaches  reporter lines and human primary cell culture methods  we provide evidence that Interleukin 11 signaling limits endothelial to myofibroblast transdifferentiation and maintains a pro regenerative niche to promote cardiac regeneration. Altogether  our data reveal a vital role for endothelial Interleukin 11/Stat3 signaling in containing injury induced cardiac fibrosis. Overall design: 96 hours post cryoinjury cardiac ventricle samples from adult il11ra mutant vs. wild type were analyzed in duplicates with each replicate derived by pooling 2 ventricles. 24 hours post amputation caudal fin samples from adult il11ra mutant vs. wild type were analyzed in triplicates with each replicate derived from single fins.,,pubmed:34516874,,il11ra mutant fin  24 hpa  rep3,GSM4911940,,tissue:Caudal fin|developmental stage:adult|genotype:il11ra mutant|treatment:fin amputation|time point:24 hpa,il11ra mutant fin  24 hpa  rep3,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus Ensembl zebrafish genome version danRer11 GRCz11 using STAR 2.7.3a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.26. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: danRer11 Supplementary files format and content: library size normalized counts,Caudal fin,,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,,developmental stage:adult|genotype:il11ra mutant|treatment:fin amputation|time point:24 hpa,GSM4911940,GSM4911940: il11ra mutant fin  24 hpa  rep3; Danio rerio; RNA Seq,GSM4911940,,1,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,GEO Accession:GSM4911940,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP292933,,,Reischauer_Mut3_R1.fastq.gz,fastq,1851680943.0,25042899.0,GSM4911940 r1,0:73.94 1:0,A:487052421;C:413627060;G:426276923;T:524716682;N:7857,73,0,,,487052421,413627060,426276923,524716682,7857,SRX9522192,SRS7729391,SRA1160354,GEO,MPI for heart and lung research,1,0.91637,,0.09982,,0.74241,,0.48534,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2020-11-17,Adult,Adult,Fin,Surface Structure
61954,SRR13075148,SRX9522191,SRS7729392,SRP292933,PRJNA679002,Role of Il 11 signaling in adult heart and fin regeneration in zebrafish,GSE161647,Transcriptome Analysis,In adult mammals  tissue damage post myocardial infarction induces myofibroblast differentiation and the formation of a permanent  functionally inert scar.  However  the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood.  Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis post tissue damage  including in the heart.  Here  employing comparative expression profiling coupled with loss of function approaches  we identified the canonical Interleukin 11/Stat3 signaling axis as a core component of regeneration in zebrafish.  Notably  animals with loss of Interleukin 11 receptor Il11ra function reach maturity without xxx developmental defects  but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar  similar to what is observed in adult mammals.  Using zebrafish fate mapping approaches  reporter lines and human primary cell culture methods  we provide evidence that Interleukin 11 signaling limits endothelial to myofibroblast transdifferentiation and maintains a pro regenerative niche to promote cardiac regeneration. Altogether  our data reveal a vital role for endothelial Interleukin 11/Stat3 signaling in containing injury induced cardiac fibrosis. Overall design: 96 hours post cryoinjury cardiac ventricle samples from adult il11ra mutant vs. wild type were analyzed in duplicates with each replicate derived by pooling 2 ventricles. 24 hours post amputation caudal fin samples from adult il11ra mutant vs. wild type were analyzed in triplicates with each replicate derived from single fins.,,pubmed:34516874,,il11ra mutant fin  24 hpa  rep2,GSM4911939,,tissue:Caudal fin|developmental stage:adult|genotype:il11ra mutant|treatment:fin amputation|time point:24 hpa,il11ra mutant fin  24 hpa  rep2,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus Ensembl zebrafish genome version danRer11 GRCz11 using STAR 2.7.3a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.26. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: danRer11 Supplementary files format and content: library size normalized counts,Caudal fin,,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,,developmental stage:adult|genotype:il11ra mutant|treatment:fin amputation|time point:24 hpa,GSM4911939,GSM4911939: il11ra mutant fin  24 hpa  rep2; Danio rerio; RNA Seq,GSM4911939,,1,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,GEO Accession:GSM4911939,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP292933,,,Reischauer_Mut2_R1.fastq.gz,fastq,2038104304.0,27531234.0,GSM4911939 r1,0:74.03 1:0,A:539462021;C:452986503;G:465883483;T:579763891;N:8406,74,0,,,539462021,452986503,465883483,579763891,8406,SRX9522191,SRS7729392,SRA1160354,GEO,MPI for heart and lung research,1,0.90834,,0.09857,,0.74154,,0.47755,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2020-11-17,Adult,Adult,Fin,Surface Structure
61955,SRR13075147,SRX9522190,SRS7729390,SRP292933,PRJNA679002,Role of Il 11 signaling in adult heart and fin regeneration in zebrafish,GSE161647,Transcriptome Analysis,In adult mammals  tissue damage post myocardial infarction induces myofibroblast differentiation and the formation of a permanent  functionally inert scar.  However  the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood.  Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis post tissue damage  including in the heart.  Here  employing comparative expression profiling coupled with loss of function approaches  we identified the canonical Interleukin 11/Stat3 signaling axis as a core component of regeneration in zebrafish.  Notably  animals with loss of Interleukin 11 receptor Il11ra function reach maturity without xxx developmental defects  but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar  similar to what is observed in adult mammals.  Using zebrafish fate mapping approaches  reporter lines and human primary cell culture methods  we provide evidence that Interleukin 11 signaling limits endothelial to myofibroblast transdifferentiation and maintains a pro regenerative niche to promote cardiac regeneration. Altogether  our data reveal a vital role for endothelial Interleukin 11/Stat3 signaling in containing injury induced cardiac fibrosis. Overall design: 96 hours post cryoinjury cardiac ventricle samples from adult il11ra mutant vs. wild type were analyzed in duplicates with each replicate derived by pooling 2 ventricles. 24 hours post amputation caudal fin samples from adult il11ra mutant vs. wild type were analyzed in triplicates with each replicate derived from single fins.,,pubmed:34516874,,il11ra mutant fin  24 hpa  rep1,GSM4911938,,tissue:Caudal fin|developmental stage:adult|genotype:il11ra mutant|treatment:fin amputation|time point:24 hpa,il11ra mutant fin  24 hpa  rep1,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus Ensembl zebrafish genome version danRer11 GRCz11 using STAR 2.7.3a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.26. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: danRer11 Supplementary files format and content: library size normalized counts,Caudal fin,,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,,developmental stage:adult|genotype:il11ra mutant|treatment:fin amputation|time point:24 hpa,GSM4911938,GSM4911938: il11ra mutant fin  24 hpa  rep1; Danio rerio; RNA Seq,GSM4911938,,1,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,GEO Accession:GSM4911938,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP292933,,,Reischauer_Mut1_R1.fastq.gz,fastq,1531546717.0,20622961.0,GSM4911938 r1,0:74.26 1:0,A:407261383;C:338321295;G:350917574;T:435041628;N:4837,74,0,,,407261383,338321295,350917574,435041628,4837,SRX9522190,SRS7729390,SRA1160354,GEO,MPI for heart and lung research,1,0.90833,,0.10892,,0.77928,,0.48087,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2020-11-17,Adult,Adult,Fin,Surface Structure
61956,SRR13075146,SRX9522189,SRS7729389,SRP292933,PRJNA679002,Role of Il 11 signaling in adult heart and fin regeneration in zebrafish,GSE161647,Transcriptome Analysis,In adult mammals  tissue damage post myocardial infarction induces myofibroblast differentiation and the formation of a permanent  functionally inert scar.  However  the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood.  Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis post tissue damage  including in the heart.  Here  employing comparative expression profiling coupled with loss of function approaches  we identified the canonical Interleukin 11/Stat3 signaling axis as a core component of regeneration in zebrafish.  Notably  animals with loss of Interleukin 11 receptor Il11ra function reach maturity without xxx developmental defects  but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar  similar to what is observed in adult mammals.  Using zebrafish fate mapping approaches  reporter lines and human primary cell culture methods  we provide evidence that Interleukin 11 signaling limits endothelial to myofibroblast transdifferentiation and maintains a pro regenerative niche to promote cardiac regeneration. Altogether  our data reveal a vital role for endothelial Interleukin 11/Stat3 signaling in containing injury induced cardiac fibrosis. Overall design: 96 hours post cryoinjury cardiac ventricle samples from adult il11ra mutant vs. wild type were analyzed in duplicates with each replicate derived by pooling 2 ventricles. 24 hours post amputation caudal fin samples from adult il11ra mutant vs. wild type were analyzed in triplicates with each replicate derived from single fins.,,pubmed:34516874,,Wild type fin  24 hpa  rep3,GSM4911937,,tissue:Caudal fin|developmental stage:adult|genotype:wild type|treatment:fin amputation|time point:24 hpa,Wild type fin  24 hpa  rep3,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus Ensembl zebrafish genome version danRer11 GRCz11 using STAR 2.7.3a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.26. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: danRer11 Supplementary files format and content: library size normalized counts,Caudal fin,,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,,developmental stage:adult|genotype:wild type|treatment:fin amputation|time point:24 hpa,GSM4911937,GSM4911937: Wild type fin  24 hpa  rep3; Danio rerio; RNA Seq,GSM4911937,,1,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,GEO Accession:GSM4911937,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP292933,,,Reischauer_WT3_R1.fastq.gz,fastq,2048531484.0,27689871.0,GSM4911937 r1,0:73.98 1:0,A:535652814;C:462058885;G:474011200;T:576800188;N:8397,73,0,,,535652814,462058885,474011200,576800188,8397,SRX9522189,SRS7729389,SRA1160354,GEO,MPI for heart and lung research,1,0.93148,,0.08066,,0.7516,,0.4515,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2020-11-17,Adult,Adult,Fin,Surface Structure
61957,SRR13075145,SRX9522188,SRS7729388,SRP292933,PRJNA679002,Role of Il 11 signaling in adult heart and fin regeneration in zebrafish,GSE161647,Transcriptome Analysis,In adult mammals  tissue damage post myocardial infarction induces myofibroblast differentiation and the formation of a permanent  functionally inert scar.  However  the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood.  Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis post tissue damage  including in the heart.  Here  employing comparative expression profiling coupled with loss of function approaches  we identified the canonical Interleukin 11/Stat3 signaling axis as a core component of regeneration in zebrafish.  Notably  animals with loss of Interleukin 11 receptor Il11ra function reach maturity without xxx developmental defects  but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar  similar to what is observed in adult mammals.  Using zebrafish fate mapping approaches  reporter lines and human primary cell culture methods  we provide evidence that Interleukin 11 signaling limits endothelial to myofibroblast transdifferentiation and maintains a pro regenerative niche to promote cardiac regeneration. Altogether  our data reveal a vital role for endothelial Interleukin 11/Stat3 signaling in containing injury induced cardiac fibrosis. Overall design: 96 hours post cryoinjury cardiac ventricle samples from adult il11ra mutant vs. wild type were analyzed in duplicates with each replicate derived by pooling 2 ventricles. 24 hours post amputation caudal fin samples from adult il11ra mutant vs. wild type were analyzed in triplicates with each replicate derived from single fins.,,pubmed:34516874,,Wild type fin  24 hpa  rep2,GSM4911936,,tissue:Caudal fin|developmental stage:adult|genotype:wild type|treatment:fin amputation|time point:24 hpa,Wild type fin  24 hpa  rep2,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus Ensembl zebrafish genome version danRer11 GRCz11 using STAR 2.7.3a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.26. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: danRer11 Supplementary files format and content: library size normalized counts,Caudal fin,,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,,developmental stage:adult|genotype:wild type|treatment:fin amputation|time point:24 hpa,GSM4911936,GSM4911936: Wild type fin  24 hpa  rep2; Danio rerio; RNA Seq,GSM4911936,,1,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,GEO Accession:GSM4911936,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP292933,,,Reischauer_WT2_R1.fastq.gz,fastq,2321703525.0,31306353.0,GSM4911936 r1,0:74.16 1:0,A:595815579;C:531081067;G:543179238;T:651618366;N:9275,74,0,,,595815579,531081067,543179238,651618366,9275,SRX9522188,SRS7729388,SRA1160354,GEO,MPI for heart and lung research,1,0.93426,,0.07768,,0.74826,,0.4649,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2020-11-17,Adult,Adult,Fin,Surface Structure
61958,SRR13075144,SRX9522187,SRS7729387,SRP292933,PRJNA679002,Role of Il 11 signaling in adult heart and fin regeneration in zebrafish,GSE161647,Transcriptome Analysis,In adult mammals  tissue damage post myocardial infarction induces myofibroblast differentiation and the formation of a permanent  functionally inert scar.  However  the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood.  Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis post tissue damage  including in the heart.  Here  employing comparative expression profiling coupled with loss of function approaches  we identified the canonical Interleukin 11/Stat3 signaling axis as a core component of regeneration in zebrafish.  Notably  animals with loss of Interleukin 11 receptor Il11ra function reach maturity without xxx developmental defects  but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar  similar to what is observed in adult mammals.  Using zebrafish fate mapping approaches  reporter lines and human primary cell culture methods  we provide evidence that Interleukin 11 signaling limits endothelial to myofibroblast transdifferentiation and maintains a pro regenerative niche to promote cardiac regeneration. Altogether  our data reveal a vital role for endothelial Interleukin 11/Stat3 signaling in containing injury induced cardiac fibrosis. Overall design: 96 hours post cryoinjury cardiac ventricle samples from adult il11ra mutant vs. wild type were analyzed in duplicates with each replicate derived by pooling 2 ventricles. 24 hours post amputation caudal fin samples from adult il11ra mutant vs. wild type were analyzed in triplicates with each replicate derived from single fins.,,pubmed:34516874,,Wild type fin  24 hpa  rep1,GSM4911935,,tissue:Caudal fin|developmental stage:adult|genotype:wild type|treatment:fin amputation|time point:24 hpa,Wild type fin  24 hpa  rep1,The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus Ensembl zebrafish genome version danRer11 GRCz11 using STAR 2.7.3a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.26. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: danRer11 Supplementary files format and content: library size normalized counts,Caudal fin,,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,,developmental stage:adult|genotype:wild type|treatment:fin amputation|time point:24 hpa,GSM4911935,GSM4911935: Wild type fin  24 hpa  rep1; Danio rerio; RNA Seq,GSM4911935,,1,Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in  80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina,GEO Accession:GSM4911935,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP292933,,,Reischauer_WT1_R1.fastq.gz,fastq,1653887807.0,22260443.0,GSM4911935 r1,0:74.30 1:0,A:433508052;C:372348710;G:380715605;T:467309125;N:6315,74,0,,,433508052,372348710,380715605,467309125,6315,SRX9522187,SRS7729387,SRA1160354,GEO,MPI for heart and lung research,1,0.92899,,0.0857,,0.77835,,0.47041,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2020-11-17,Adult,Adult,Fin,Surface Structure
65645,SRR15458886,SRX11758247,SRS9777785,SRP332539,PRJNA754591,Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes,GSE182113,Transcriptome Analysis,We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish,,pubmed:34622167,,Uncut fin fold rep3,GSM5518678,,source name:larval fin fold|tissue:larval fin fold|treatment:uncut,Uncut fin fold rep3,Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts,larval fin fold,,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,,tissue:larval fin fold|treatment:uncut,GSM5518678,GSM5518678: Uncut fin fold rep3; Danio rerio; RNA Seq,GSM5518678,,1,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,GEO Accession:GSM5518678,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP332539,,,unDMSO-3_S9_L008_R1_001.fastq.gz,fastq,1463248650.0,28691150.0,GSM5518678 r1,0:51 1:0,A:397962408;C:373148163;G:352701142;T:339050095;N:386842,51,0,,,397962408,373148163,352701142,339050095,386842,SRX11758247,SRS9777785,SRA1278109,GEO,National Tsing-Hua University,1,0.91418,,0.06051,,0.77958,,0.45543,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2021-08-14,Larval,Larval,Fin,Surface Structure
65646,SRR15458885,SRX11758246,SRS9777786,SRP332539,PRJNA754591,Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes,GSE182113,Transcriptome Analysis,We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish,,pubmed:34622167,,Uncut fin fold rep2,GSM5518677,,source name:larval fin fold|tissue:larval fin fold|treatment:uncut,Uncut fin fold rep2,Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts,larval fin fold,,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,,tissue:larval fin fold|treatment:uncut,GSM5518677,GSM5518677: Uncut fin fold rep2; Danio rerio; RNA Seq,GSM5518677,,1,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,GEO Accession:GSM5518677,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP332539,,,unDMSO-2_S5_L008_R1_001.fastq.gz,fastq,1534053174.0,30079474.0,GSM5518677 r1,0:51 1:0,A:375567653;C:393670046;G:387649149;T:376851052;N:315274,51,0,,,375567653,393670046,387649149,376851052,315274,SRX11758246,SRS9777786,SRA1278109,GEO,National Tsing-Hua University,1,0.95025,,0.06073,,0.7245,,0.46029,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2021-08-14,Larval,Larval,Fin,Surface Structure
65647,SRR15458884,SRX11758245,SRS9777784,SRP332539,PRJNA754591,Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes,GSE182113,Transcriptome Analysis,We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish,,pubmed:34622167,,Uncut fin fold rep1,GSM5518676,,source name:larval fin fold|tissue:larval fin fold|treatment:uncut,Uncut fin fold rep1,Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts,larval fin fold,,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,,tissue:larval fin fold|treatment:uncut,GSM5518676,GSM5518676: Uncut fin fold rep1; Danio rerio; RNA Seq,GSM5518676,,1,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,GEO Accession:GSM5518676,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP332539,,,unDMSO-1_S1_L008_R1_001.fastq.gz,fastq,1174809939.0,23035489.0,GSM5518676 r1,0:51 1:0,A:288665248;C:299039651;G:296219712;T:290639919;N:245409,51,0,,,288665248,299039651,296219712,290639919,245409,SRX11758245,SRS9777784,SRA1278109,GEO,National Tsing-Hua University,1,0.94689,,0.06026,,0.73204,,0.44369,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2021-08-14,Larval,Larval,Fin,Surface Structure
65648,SRR15458889,SRX11758244,SRS9777782,SRP332539,PRJNA754591,Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes,GSE182113,Transcriptome Analysis,We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish,,pubmed:34622167,,4hpa rep3,GSM5518681,,source name:larval fin fold|tissue:larval fin fold|treatment:4h post amputation,4hpa rep3,Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts,larval fin fold,,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,,tissue:larval fin fold|treatment:4h post amputation,GSM5518681,GSM5518681: 4hpa rep3; Danio rerio; RNA Seq,GSM5518681,,1,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,GEO Accession:GSM5518681,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP332539,,,4hDMSO-3_S11_L008_R1_001.fastq.gz,fastq,1550745576.0,30406776.0,GSM5518681 r1,0:51 1:0,A:387174249;C:402754112;G:383357587;T:377128496;N:331132,51,0,,,387174249,402754112,383357587,377128496,331132,SRX11758244,SRS9777782,SRA1278109,GEO,National Tsing-Hua University,1,0.9503,,0.06384,,0.71723,,0.4534,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2021-08-14,Larval,Larval,Fin,Surface Structure
65649,SRR15458888,SRX11758243,SRS9777783,SRP332539,PRJNA754591,Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes,GSE182113,Transcriptome Analysis,We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish,,pubmed:34622167,,4hpa rep2,GSM5518680,,source name:larval fin fold|tissue:larval fin fold|treatment:4h post amputation,4hpa rep2,Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts,larval fin fold,,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,,tissue:larval fin fold|treatment:4h post amputation,GSM5518680,GSM5518680: 4hpa rep2; Danio rerio; RNA Seq,GSM5518680,,1,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,GEO Accession:GSM5518680,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP332539,,,4hDMSO-2_S7_L008_R1_001.fastq.gz,fastq,1410871038.0,27664138.0,GSM5518680 r1,0:51 1:0,A:366166995;C:357462752;G:343178962;T:343741181;N:321148,51,0,,,366166995,357462752,343178962,343741181,321148,SRX11758243,SRS9777783,SRA1278109,GEO,National Tsing-Hua University,1,0.93684,,0.06834,,0.71705,,0.46343,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2021-08-14,Larval,Larval,Fin,Surface Structure
65650,SRR15458887,SRX11758242,SRS9777781,SRP332539,PRJNA754591,Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes,GSE182113,Transcriptome Analysis,We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold Overall design: Larval fin fold mRNA profiles of 3 dpf control and fin amputated zebrafish,,pubmed:34622167,,4hpa rep1,GSM5518679,,source name:larval fin fold|tissue:larval fin fold|treatment:4h post amputation,4hpa rep1,Tophat and Cufflinks DESeq2 Differential Analysis in R Supplementary files format and content: raw count and normalized counts,larval fin fold,,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,,tissue:larval fin fold|treatment:4h post amputation,GSM5518679,GSM5518679: 4hpa rep1; Danio rerio; RNA Seq,GSM5518679,,1,Fin folds were collected in cold PBS  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. TruSeq RNA Library Prep Kit v2 Illumina,GEO Accession:GSM5518679,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP332539,,,4hDMSO-1_S3_L008_R1_001.fastq.gz,fastq,1262762193.0,24760043.0,GSM5518679 r1,0:51 1:0,A:314766829;C:319337908;G:315265233;T:313124694;N:267529,51,0,,,314766829,319337908,315265233,313124694,267529,SRX11758242,SRS9777781,SRA1278109,GEO,National Tsing-Hua University,1,0.9491,,0.0613,,0.7135,,0.45795,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Taiwan,2021-08-14,Larval,Larval,Fin,Surface Structure
67811,SRR17312072,SRX13488771,SRS11384713,SRP352163,PRJNA791663,Single cell resolution of MET  and EMT like programs in osteoblasts during zebrafish fin regeneration,GSE192498,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse  mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components  or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump  and in differentiating osteoblastic cells in the regenerate  the latter of which are enriched in EMT signatures. We also show that esrp1  a regulator of alternative splicing in epithelial cells that is associated with MET  is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration  and supports the contribution of MET  and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3,,pubmed:35169687,,5 dpa,GSM5747967,,source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:5 dy post amputation|molecule subtype:nuclear RNA,5 dpa,Base calls were converted to fastq format using Illumina's bcl2fastq v2.20  tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information  while the R2 reads contain the transcriptome sequence. In the demultiplexing process  the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted  and duplicates were removed using the UMI sequence  reverse transcription RT index  and read 2 end coordinate  tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices  the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes  gene annotations  and a gene count sparse matrix for each Sample,adult caudal fin,,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,strain:AB|tissue:caudal fin|timepoint:5 dy post amputation|molecule subtype:nuclear RNA,GSM5747967,GSM5747967: 5 dpa; Danio rerio; RNA Seq,GSM5747967 r1,GSM5747967,1,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP352163,,loader:fastq load.py|options:  appendBCtoName,RK6.fq.gz,fastq,10033219500.0,100332195.0,GSM5747967 r1,0:100,A:3474987443;C:1873037986;G:1979251566;T:2705812216;N:130289,100,,,,3474987443,1873037986,1979251566,2705812216,130289,SRX13488771,SRS11384713,SRA1347953,"Kwon Lab, Orthopedics &amp; Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington","Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington",1,0.71399,,0.43822,,0.84161,,0.72626,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2021-12-22,Adult,Adult,Fin,Surface Structure
67812,SRR17312073,SRX13488770,SRS11384711,SRP352163,PRJNA791663,Single cell resolution of MET  and EMT like programs in osteoblasts during zebrafish fin regeneration,GSE192498,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse  mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components  or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump  and in differentiating osteoblastic cells in the regenerate  the latter of which are enriched in EMT signatures. We also show that esrp1  a regulator of alternative splicing in epithelial cells that is associated with MET  is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration  and supports the contribution of MET  and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3,,pubmed:35169687,,3 dpa,GSM5747966,,source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA,3 dpa,Base calls were converted to fastq format using Illumina's bcl2fastq v2.20  tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information  while the R2 reads contain the transcriptome sequence. In the demultiplexing process  the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted  and duplicates were removed using the UMI sequence  reverse transcription RT index  and read 2 end coordinate  tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices  the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes  gene annotations  and a gene count sparse matrix for each Sample,adult caudal fin,,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA,GSM5747966,GSM5747966: 3 dpa; Danio rerio; RNA Seq,GSM5747966 r1,GSM5747966,1,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP352163,,loader:fastq load.py|options:  appendBCtoName,RK5.fq.gz,fastq,7765549400.0,77655494.0,GSM5747966 r1,0:100,A:2667279419;C:1502480624;G:1625734956;T:1969954499;N:99902,100,,,,2667279419,1502480624,1625734956,1969954499,99902,SRX13488770,SRS11384711,SRA1347953,"Kwon Lab, Orthopedics &amp; Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington","Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington",1,0.65628,,0.27575,,0.84918,,0.73771,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2021-12-22,Adult,Adult,Fin,Surface Structure
67813,SRR17312074,SRX13488769,SRS11384712,SRP352163,PRJNA791663,Single cell resolution of MET  and EMT like programs in osteoblasts during zebrafish fin regeneration,GSE192498,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse  mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components  or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump  and in differentiating osteoblastic cells in the regenerate  the latter of which are enriched in EMT signatures. We also show that esrp1  a regulator of alternative splicing in epithelial cells that is associated with MET  is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration  and supports the contribution of MET  and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3,,pubmed:35169687,,3 dpa pilot,GSM5747965,,source name:adult caudal fin|strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA,3 dpa pilot,Base calls were converted to fastq format using Illumina's bcl2fastq v2.20  tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information  while the R2 reads contain the transcriptome sequence. In the demultiplexing process  the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted  and duplicates were removed using the UMI sequence  reverse transcription RT index  and read 2 end coordinate  tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices  the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes  gene annotations  and a gene count sparse matrix for each Sample,adult caudal fin,,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,strain:AB|tissue:caudal fin|timepoint:3 dy post amputation|molecule subtype:nuclear RNA,GSM5747965,GSM5747965: 3 dpa pilot; Danio rerio; RNA Seq,GSM5747965 r1,GSM5747965,1,Fin tissues were collected and immediately frozen at  80C. Nuclei were extracted  fixed in 4% paraformaldehyde  and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed  with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription  the Quick Ligation kit New England Biolabs was used in place of T4 ligase  and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP352163,,loader:fastq load.py|options:  appendBCtoName,RK.1.fq.gz,fastq,4869714300.0,48697143.0,GSM5747965 r1,0:100,A:1531034092;C:971890195;G:1007416432;T:1359257595;N:115986,100,,,,1531034092,971890195,1007416432,1359257595,115986,SRX13488769,SRS11384712,SRA1347953,"Kwon Lab, Orthopedics &amp; Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington","Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington",1,0.60845,,0.32412,,0.84916,,0.72554,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2021-12-22,Adult,Adult,Fin,Surface Structure