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
282,DRR179616,DRX170142,DRS185505,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 2,Fin xanthophore 03,SAMD00172019,,sample name:Zebrafish pigment cell 06|cell type:Xanthophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172019,DRX170142,Zebrafish fin xanthophore 01,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</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>,DRP007318,Ion Torrent PGM sequencing of SAMD00172019,,,,376558775.0,1624500.0,DRR179616,0:231.80,A:107837072;C:79508449;G:79372899;T:109840355;N:0,231,,,,107837072,79508449,79372899,109840355,0,DRX170142,DRS185505,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.86944,,0.10951,,0.90425,,0.59385,,311,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
283,DRR179615,DRX170141,DRS185504,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 1,Fin xanthophore 02,SAMD00172018,,sample name:Zebrafish pigment cell 05|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172018,DRX170141,Zebrafish fin xanthophore 01,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>243</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>,DRP007318,Ion Torrent PGM sequencing of SAMD00172018,,,,515115515.0,2124170.0,DRR179615,0:242.50,A:138421982;C:119032803;G:119412227;T:138248503;N:0,242,,,,138421982,119032803,119412227,138248503,0,DRX170141,DRS185504,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.88998,,0.05858,,0.88051,,0.50917,,284,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
284,DRR179614,DRX170140,DRS185503,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 1,Fin xanthophore 01,SAMD00172017,,sample name:Zebrafish pigment cell 04|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172017,DRX170140,Zebrafish fin xanthophore 01,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>247</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>,DRP007318,Ion Torrent PGM sequencing of SAMD00172017,,,,371242152.0,1504407.0,DRR179614,0:246.77,A:99341086;C:86126839;G:86264882;T:99509345;N:0,246,,,,99341086,86126839,86264882,99509345,0,DRX170140,DRS185503,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.88672,,0.06422,,0.85679,,0.5066,,56,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
285,DRR179613,DRX170139,DRS185502,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 2,Fin melanophore 03,SAMD00172016,,sample name:Zebrafish pigment cell 03|cell type:Melanophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172016,DRX170139,Zebrafish fin melanophore 03,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>248</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>,DRP007318,Ion Torrent PGM sequencing of SAMD00172016,,,,342802993.0,1585538.0,DRR179613,0:216.21,A:90833658;C:80789744;G:80463233;T:90716358;N:0,216,,,,90833658,80789744,80463233,90716358,0,DRX170139,DRS185502,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.8312,,0.03528,,0.88605,,0.47299,,285,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
286,DRR179612,DRX170138,DRS185501,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 1,Fin melanophore 02,SAMD00172015,,sample name:Zebrafish pigment cell 02|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172015,DRX170138,Zebrafish fin melanophore 02,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</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>,DRP007318,Ion Torrent PGM sequencing of SAMD00172015,,,,538412675.0,2168231.0,DRR179612,0:248.32,A:147128403;C:121854818;G:121564109;T:147865345;N:0,248,,,,147128403,121854818,121564109,147865345,0,DRX170138,DRS185501,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.89106,,0.07081,,0.89286,,0.5935,,283,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
287,DRR179611,DRX170137,DRS185500,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 1,Fin melanophore 01,SAMD00172014,,sample name:Zebrafish pigment cell 01|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172014,DRX170137,Zebrafish fin melanophore 01,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</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>,DRP007318,Ion Torrent PGM sequencing of SAMD00172014,,,,282446840.0,1311431.0,DRR179611,0:215.37,A:74927237;C:66575483;G:66161471;T:74782649;N:0,215,,,,74927237,66575483,66161471,74782649,0,DRX170137,DRS185500,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.85938,,0.0335,,0.89248,,0.58813,,274,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
288,DRR224554,DRX214839,DRS236362,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish Adult C,SAMD00222585,,sample name:Adult C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222585,DRX214839,Adult C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222585,,,,11727505800.0,58637529.0,DRR224554,0:100 1:100,A:3137648588;C:2705013210;G:3191753451;T:2692963496;N:127055,100,100,,,3137648588,2705013210,3191753451,2692963496,127055,DRX214839,DRS236362,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.95934,0.93156,0.03853,0.0394,0.72683,0.74625,0.45812,0.47098,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Adult,Adult,Fin,Surface Structure
289,DRR224553,DRX214838,DRS236361,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish Adult B,SAMD00222584,,sample name:Adult B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222584,DRX214838,Adult B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222584,,,,22010855600.0,110054278.0,DRR224553,0:100 1:100,A:5511440112;C:5498539659;G:5546758172;T:5453879750;N:237907,100,100,,,5511440112,5498539659,5546758172,5453879750,237907,DRX214838,DRS236361,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.95774,0.95394,0.04568,0.04411,0.70701,0.70881,0.47041,0.47938,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Adult,Adult,Fin,Surface Structure
290,DRR224552,DRX214837,DRS236360,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish Adult A,SAMD00222583,,sample name:Adult A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222583,DRX214837,Adult A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222583,,,,17683281000.0,88416405.0,DRR224552,0:100 1:100,A:4386756926;C:4479415938;G:4578796094;T:4238125580;N:186462,100,100,,,4386756926,4479415938,4578796094,4238125580,186462,DRX214837,DRS236360,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.95974,0.95566,0.05237,0.05086,0.74357,0.74742,0.48578,0.49971,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Adult,Adult,Fin,Surface Structure
3759,ERR1294279,ERX1365625,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9,vbu13,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu13_GCCAAT_L008_R1_001.fastq.gz,fastq,2376143675.0,23526175.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9,0:101,A:655940769;C:534990399;G:527934646;T:655773043;N:1504818,101,,,,655940769,534990399,527934646,655773043,1504818,ERX1365625,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95443,,0.10666,,0.73176,,0.50978,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3760,ERR1294278,ERX1365624,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8,vbu12,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu12_GTGAAA_L008_R1_001.fastq.gz,fastq,1449181835.0,14348335.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8,0:101,A:399518584;C:327615685;G:323868050;T:397240465;N:939051,101,,,,399518584,327615685,323868050,397240465,939051,ERX1365624,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95893,,0.09315,,0.73464,,0.48744,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3761,ERR1294277,ERX1365623,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7,vbu11,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu11_GTCCGC_L008_R1_001.fastq.gz,fastq,1455235169.0,14408269.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7,0:101,A:392100064;C:337980617;G:331091626;T:393178582;N:884280,101,,,,392100064,337980617,331091626,393178582,884280,ERX1365623,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95485,,0.08016,,0.72845,,0.47549,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3762,ERR1294276,ERX1365622,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6,ve13,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve13_CCGTCC_L008_R1_001.fastq.gz,fastq,1029294030.0,10191030.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6,0:101,A:284612731;C:231451012;G:228443320;T:284135536;N:651431,101,,,,284612731,231451012,228443320,284135536,651431,ERX1365622,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.93287,,0.10726,,0.72585,,0.4913,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3763,ERR1294275,ERX1365621,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5,ve12,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve12_ATGTCA_L008_R1_001.fastq.gz,fastq,1446322222.0,14320022.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5,0:101,A:400821160;C:324210104;G:320286425;T:400078485;N:926048,101,,,,400821160,324210104,320286425,400078485,926048,ERX1365621,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.92778,,0.09489,,0.73093,,0.48493,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3764,ERR1294274,ERX1365620,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4,ve11,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve11_AGTTCC_L008_R1_001.fastq.gz,fastq,2117238861.0,20962761.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4,0:101,A:591654664;C:469803769;G:462550117;T:591863795;N:1366516,101,,,,591654664,469803769,462550117,591863795,1366516,ERX1365620,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.93146,,0.09666,,0.73501,,0.48749,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3765,ERR1294273,ERX1365619,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3,wt3,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt3_AGTCAA_L008_R1_001.fastq.gz,fastq,2631687411.0,26056311.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3,0:101,A:734843629;C:584316000;G:577487406;T:733356850;N:1683526,101,,,,734843629,584316000,577487406,733356850,1683526,ERX1365619,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95114,,0.1036,,0.72474,,0.48261,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3766,ERR1294272,ERX1365618,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2,wt2,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt2_CTTGTA_L008_R1_001.fastq.gz,fastq,2093443463.0,20727163.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2,0:101,A:607582034;C:442802229;G:437957089;T:603752294;N:1349817,101,,,,607582034,442802229,437957089,603752294,1349817,ERX1365618,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.94792,,0.10892,,0.73277,,0.51067,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3767,ERR1294271,ERX1365617,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1,wt1,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt1_CAGATC_L008_R1_001.fastq.gz,fastq,1701561241.0,16847141.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1,0:101,A:505358711;C:348893979;G:343445186;T:502880170;N:983195,101,,,,505358711,348893979,343445186,502880170,983195,ERX1365617,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.94565,,0.13032,,0.73669,,0.50473,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
9170,ERR216332,ERX190997,ERS094086,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689285,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689285|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#6,4927108,Illumina sequencing of library 4927108  constructed from sample accession ERS094086 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence GCCAATGT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#6.bam,bam,3849223200.0,25661488.0,SC RUN 7896 6#6,0:75 1:75,A:1052343872;C:867977827;G:867966925;T:1060514703;N:419873,75,75,,,1052343872,867977827,867966925,1060514703,419873,ERX190997,ERS094086,ERA182034,SC,Wellcome Sanger Institute,2,0.94843,0.9504,0.09374,0.09366,0.71421,0.71916,0.5306,0.52809,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9171,ERR216331,ERX190996,ERS094085,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689286,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:15Z|External Id:SAMEA1689286|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:15Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#5,4927107,Illumina sequencing of library 4927107  constructed from sample accession ERS094085 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence ACAGTGGT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#5.bam,bam,5957027700.0,39713518.0,SC RUN 7896 6#5,0:75 1:75,A:1634176455;C:1344899134;G:1345048404;T:1632256963;N:646744,75,75,,,1634176455,1344899134,1345048404,1632256963,646744,ERX190996,ERS094085,ERA182034,SC,Wellcome Sanger Institute,2,0.94169,0.94387,0.09489,0.09587,0.69406,0.69869,0.51459,0.51918,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9172,ERR216330,ERX190995,ERS094084,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689283,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689283|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#4,4927106,Illumina sequencing of library 4927106  constructed from sample accession ERS094084 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence TGACCACT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#4.bam,bam,4130918700.0,27539458.0,SC RUN 7896 6#4,0:75 1:75,A:1129107864;C:933544249;G:934913323;T:1132901907;N:451357,75,75,,,1129107864,933544249,934913323,1132901907,451357,ERX190995,ERS094084,ERA182034,SC,Wellcome Sanger Institute,2,0.94225,0.94433,0.09272,0.09299,0.70043,0.70534,0.51333,0.52182,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9173,ERR216329,ERX190994,ERS094083,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689282,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689282|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#3,4927105,Illumina sequencing of library 4927105  constructed from sample accession ERS094083 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence TTAGGCAT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#3.bam,bam,5102725800.0,34018172.0,SC RUN 7896 6#3,0:75 1:75,A:1400946711;C:1145033579;G:1143298888;T:1412890130;N:556492,75,75,,,1400946711,1145033579,1143298888,1412890130,556492,ERX190994,ERS094083,ERA182034,SC,Wellcome Sanger Institute,2,0.93688,0.93952,0.07363,0.07321,0.69645,0.70161,0.48708,0.48926,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9174,ERR216328,ERX190993,ERS094082,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689281,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T10:04:12Z|ENA LAST UPDATE:2018 03 08T15:36:11Z|External Id:SAMEA1689281|INSDC center name:SC|INSDC first public:2013 01 07T10:04:12Z|INSDC last update:2018 03 08T15:36:11Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#2,4927104,Illumina sequencing of library 4927104  constructed from sample accession ERS094082 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence CGATGTTT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#2.bam,bam,4350577950.0,29003853.0,SC RUN 7896 6#2,0:75 1:75,A:1214100125;C:955724962;G:954429461;T:1225838270;N:485132,75,75,,,1214100125,955724962,954429461,1225838270,485132,ERX190993,ERS094082,ERA182034,SC,Wellcome Sanger Institute,2,0.92911,0.93026,0.0749,0.07514,0.69418,0.69775,0.48934,0.49,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9175,ERR216327,ERX190992,ERS094081,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689284,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689284|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#1,4927103,Illumina sequencing of library 4927103  constructed from sample accession ERS094081 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence ATCACGTT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#1.bam,bam,5063629350.0,33757529.0,SC RUN 7896 6#1,0:75 1:75,A:1416301768;C:1110273098;G:1105481234;T:1431015934;N:557316,75,75,,,1416301768,1110273098,1105481234,1431015934,557316,ERX190992,ERS094081,ERA182034,SC,Wellcome Sanger Institute,2,0.93508,0.93634,0.11212,0.11206,0.70009,0.70538,0.50126,0.49177,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9770,ERR5838122,ERX5487778,ERS6337138,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652584,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652584|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:05 Danio rerio adult skin 5|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:05 Danio rerio adult skin 5|sex:male|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr5.1.fastq.gz S1385Nr5.2.fastq.gz,fastq fastq,6912206316.0,34306523.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5,0:100.74 1:100.74,A:1853779551;C:1607929988;G:1658402611;T:1792045990;N:48176,100,100,,,1853779551,1607929988,1658402611,1792045990,48176,ERX5487778,ERS6337138,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.96095,0.962,0.08049,0.07821,0.70654,0.70926,0.51398,0.51064,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9771,ERR5838121,ERX5487777,ERS6337136,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652582,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652582|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:04 Danio rerio adult skin 4|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:04 Danio rerio adult skin 4|sex:male|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr4.1.fastq.gz S1385Nr4.2.fastq.gz,fastq fastq,6161942050.0,30595009.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4,0:100.70 1:100.70,A:1642716052;C:1446485458;G:1490121106;T:1582576605;N:42829,100,100,,,1642716052,1446485458,1490121106,1582576605,42829,ERX5487777,ERS6337136,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.96544,0.96564,0.07368,0.07303,0.70822,0.71092,0.50154,0.50781,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9772,ERR5838120,ERX5487776,ERS6337133,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652579,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652579|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:03 Danio rerio adult skin 3|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:03 Danio rerio adult skin 3|sex:female|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr3.1.fastq.gz S1385Nr3.2.fastq.gz,fastq fastq,7422881394.0,36866805.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3,0:100.67 1:100.67,A:1950275527;C:1768648993;G:1827362519;T:1876542858;N:51497,100,100,,,1950275527,1768648993,1827362519,1876542858,51497,ERX5487776,ERS6337133,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.97031,0.97047,0.04915,0.04817,0.71459,0.71894,0.51089,0.5097,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9773,ERR5838119,ERX5487775,ERS6337132,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652578,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652578|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:02 Danio rerio adult skin 2|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:02 Danio rerio adult skin 2|sex:female|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr2.1.fastq.gz S1385Nr2.2.fastq.gz,fastq fastq,7006718028.0,34786110.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2,0:100.71 1:100.71,A:1847371523;C:1665346769;G:1712373266;T:1781565768;N:60702,100,100,,,1847371523,1665346769,1712373266,1781565768,60702,ERX5487775,ERS6337132,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.96136,0.96039,0.05872,0.05752,0.70325,0.70674,0.46717,0.48218,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9774,ERR5838118,ERX5487774,ERS6337063,ERP119543,PRJEB36360,Transcriptomic analysis of adult skin from 9 Danio species,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27,Other,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21,PUBMED:33277491,Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio  Danio aesculapii  Danio nigrofasciatus  Danio tinwini  Danio kyathit  Danio albolineatus  Danio choprae  Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end  stranded RNA Seq was then carried out.,Transcriptomic analysis of adult skin from 9 Danio species,SAMEA8652509,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652509|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:01 Danio rerio adult skin 1|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:01 Danio rerio adult skin 1|sex:male|tissue type:skin,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1,unspecified,1,TruSeq stranded mRNA Illumina,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP119543,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29,S1385Nr1.1.fastq.gz S1385Nr1.2.fastq.gz,fastq fastq,6586457266.0,32719900.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1,0:100.65 1:100.65,A:1709547533;C:1593125315;G:1617088678;T:1666650824;N:44916,100,100,,,1709547533,1593125315,1617088678,1666650824,44916,ERX5487774,ERS6337063,ERA4129786,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,2,0.9531,0.95366,0.07763,0.07567,0.71384,0.71634,0.52409,0.52475,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-03-21,Adult,Adult,Skin,Surface Structure
9970,ERR5056255,ERX4862324,ERS4959151,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,9 days post harvest,Zebrafish scale RNA seq total RNA,SAMEA7198930,University of Bristol,ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 10,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_REG3_CTTGTA_L002_R1_001.fastq.gz,fastq,435534645.0,8539895.0,ena RUN BRISTOL 08 01 2021 15:14:53:483 10,0:51 1:0,A:104994334;C:102642310;G:101303422;T:126578362;N:16217,51,0,,,104994334,102642310,101303422,126578362,16217,ERX4862324,ERS4959151,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.92322,,0.08481,,0.71997,,0.45351,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9971,ERR5056093,ERX4862162,ERS4959146,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,day x,Zebrafish scale RNA seq total RNA,SAMEA7198925,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 13:16:55:212 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_ONT1_CGATGT_L002_R1_001.fastq.gz,fastq,613101549.0,12021599.0,ena RUN BRISTOL 08 01 2021 13:16:55:212 1,0:51 1:0,A:152016801;C:139221646;G:139332264;T:182506912;N:23926,51,0,,,152016801,139221646,139332264,182506912,23926,ERX4862162,ERS4959146,ERA3206646,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.90335,,0.1072,,0.71784,,0.48228,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9972,ERR5056077,ERX4862146,ERS4959146,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,day x,Zebrafish scale RNA seq total RNA,SAMEA7198925,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198925|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 12:07:14:527 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_ONT1_CGATGT_L001_R1_001.fastq.gz,fastq,600285402.0,11770302.0,ena RUN BRISTOL 08 01 2021 12:07:14:527 1,0:51 1:0,A:148729943;C:136337224;G:136545524;T:178606078;N:66633,51,0,,,148729943,136337224,136545524,178606078,66633,ERX4862146,ERS4959146,ERA3206631,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.9026,,0.10732,,0.71683,,0.47346,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9973,ERR5056254,ERX4862323,ERS4959151,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,9 days post harvest,Zebrafish scale RNA seq total RNA,SAMEA7198930,University of Bristol,ENA first public:2021 04 20|ENA last update:2020 08 20|External Id:SAMEA7198930|INSDC center alias:BRISTOL|INSDC center name:University of Bristol|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 3|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 9,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_REG3_CTTGTA_L001_R1_001.fastq.gz,fastq,426117342.0,8355242.0,ena RUN BRISTOL 08 01 2021 15:14:53:483 9,0:51 1:0,A:102630499;C:100472291;G:99193964;T:123775368;N:45220,51,0,,,102630499,100472291,99193964,123775368,45220,ERX4862323,ERS4959151,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.92245,,0.08463,,0.71877,,0.45377,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9974,ERR5056253,ERX4862322,ERS4959150,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,9 days post harvest,Zebrafish scale RNA seq total RNA,SAMEA7198929,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 8,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_REG2_CAGATC_L002_R1_001.fastq.gz,fastq,434571714.0,8521014.0,ena RUN BRISTOL 08 01 2021 15:14:53:483 8,0:51 1:0,A:106135147;C:102194661;G:100594136;T:125630448;N:17322,51,0,,,106135147,102194661,100594136,125630448,17322,ERX4862322,ERS4959150,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.91779,,0.08112,,0.7161,,0.4437,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9975,ERR5056252,ERX4862321,ERS4959150,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,9 days post harvest,Zebrafish scale RNA seq total RNA,SAMEA7198929,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198929|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:483 7,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_REG2_CAGATC_L001_R1_001.fastq.gz,fastq,424788384.0,8329184.0,ena RUN BRISTOL 08 01 2021 15:14:53:483 7,0:51 1:0,A:103644078;C:99946940;G:98381633;T:122768121;N:47612,51,0,,,103644078,99946940,98381633,122768121,47612,ERX4862321,ERS4959150,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.91867,,0.08097,,0.71388,,0.44882,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9976,ERR5056251,ERX4862320,ERS4959149,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,9 days post harvest,Zebrafish scale RNA seq total RNA,SAMEA7198928,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198928|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_REG1_GCCAAT_L002_R1_001.fastq.gz,fastq,481725498.0,9445598.0,ena RUN BRISTOL 08 01 2021 15:14:53:482 6,0:51 1:0,A:117075718;C:111922649;G:112057835;T:140651082;N:18214,51,0,,,117075718,111922649,112057835,140651082,18214,ERX4862320,ERS4959149,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.91312,,0.08654,,0.71747,,0.46716,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9977,ERR5056250,ERX4862319,ERS4959149,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,9 days post harvest,Zebrafish scale RNA seq total RNA,SAMEA7198928,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198928|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Regenerating 1|common name:zebrafish|dev stage:Adult 1 year|sample name:Regenerating 1|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_REG1_GCCAAT_L001_R1_001.fastq.gz,fastq,471197976.0,9239176.0,ena RUN BRISTOL 08 01 2021 15:14:53:482 5,0:51 1:0,A:114367789;C:109551764;G:109678406;T:137546387;N:53630,51,0,,,114367789,109551764,109678406,137546387,53630,ERX4862319,ERS4959149,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.91412,,0.08674,,0.71632,,0.46601,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9978,ERR5056249,ERX4862318,ERS4959148,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,day x,Zebrafish scale,SAMEA7198927,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_ONT3_ACAGTG_L002_R1_001.fastq.gz,fastq,470142531.0,9218481.0,ena RUN BRISTOL 08 01 2021 15:14:53:482 4,0:51 1:0,A:116971308;C:106056823;G:107128214;T:139968487;N:17699,51,0,,,116971308,106056823,107128214,139968487,17699,ERX4862318,ERS4959148,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.90722,,0.1158,,0.72287,,0.46674,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9979,ERR5056248,ERX4862317,ERS4959148,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,day x,Zebrafish scale,SAMEA7198927,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198927|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 3|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 3|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_ONT3_ACAGTG_L001_R1_001.fastq.gz,fastq,460312587.0,9025737.0,ena RUN BRISTOL 08 01 2021 15:14:53:482 3,0:51 1:0,A:114396758;C:103865119;G:105005018;T:136994559;N:51133,51,0,,,114396758,103865119,105005018,136994559,51133,ERX4862317,ERS4959148,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.90759,,0.11359,,0.7208,,0.47232,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9980,ERR5056247,ERX4862316,ERS4959147,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,day x,Zebrafish scale RNA seq total RNA,SAMEA7198926,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_ONT2_TGACCA_L002_R1_001.fastq.gz,fastq,502898046.0,9860746.0,ena RUN BRISTOL 08 01 2021 15:14:53:482 2,0:51 1:0,A:123893447;C:111981365;G:116049412;T:150953220;N:20602,51,0,,,123893447,111981365,116049412,150953220,20602,ERX4862316,ERS4959147,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.90777,,0.11921,,0.7137,,0.48182,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
9981,ERR5056246,ERX4862315,ERS4959147,ERP123551,PRJEB39971,RNA sequencing data of ontogenetic and 9 days post harvest zebrafish scale regeneration,ena-STUDY-BRISTOL-20-08-2020-19:49:12:215-170,Other,RNA sequencing Illumina was performed on total RNA harvested from three fish using ontogenetic and 9 days post harvest elasmoid scales. Aim is to identify novel factors that regulate dermal bone formation or metabolism.,bone|elasmoidin scale|osteogenesis|regeneration|zebrafish|ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2020 08 20,,day x,Zebrafish scale RNA seq total RNA,SAMEA7198926,BRISTOL,ENA FIRST PUBLIC:2021 04 20T00:31:21Z|ENA LAST UPDATE:2020 08 20T20:11:39Z|External Id:SAMEA7198926|INSDC center name:BRISTOL|INSDC first public:2021 04 20T00:31:21Z|INSDC last update:2020 08 20T20:11:39Z|INSDC status:public|Submitter Id:Ontogenetic 2|common name:zebrafish|dev stage:Adult 1 year|sample name:Ontogenetic 2|scientific name:Danio rerio|sex:male|tissue type:Elasmoid scale,,,,,,,,,Illumina HiSeq 2500 sequencing,ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,DNase,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP123551,Illumina HiSeq 2500 sequencing,ENA FIRST PUBLIC:2021 04 20|ENA LAST UPDATE:2021 01 08,ZFG-15-01_ONT2_TGACCA_L001_R1_001.fastq.gz,fastq,491866134.0,9644434.0,ena RUN BRISTOL 08 01 2021 15:14:53:482 1,0:51 1:0,A:121063841;C:109534722;G:113610951;T:147602721;N:53899,51,0,,,121063841,109534722,113610951,147602721,53899,ERX4862315,ERS4959147,ERA3206662,University of Bristol|European Nucleotide Archive,University of Bristol,1,0.907,,0.11935,,0.71364,,0.48543,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,dnase,trueseq,bulk,unknown,unknown,,United Kingdom,2020-08-20,Adult,Adult,Scale,Surface Structure
25297,SRR25764099,SRX21486772,SRS18719072,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,Adult itgb4+ basal cells,GSM7734879,,tissue:epidermal cells|cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,Adult itgb4+ basal cells,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734879,GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq,GSM7734879 r1,GSM7734879,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz,fastq fastq,5035430000.0,12588575.0,GSM7734879 r1,0:200 1:200,A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229,200,200,,,1339392170,1117195164,1254708952,1323174485,959229,SRX21486772,SRS18719072,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01543,0.02468,0.00098,0.00102,0.99318,0.99387,0.47878,0.31718,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Adult,Adult,Skin,Surface Structure
29191,SRR27308233,SRX22985581,SRS19950789,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP /sp7+  Osteoblast  rep2,GSM7987448,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP /sp7+  Osteoblast  rep2,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987448,GSM7987448: EGFP /sp7+  Osteoblast  rep2; Danio rerio; RNA Seq,GSM7987448 r1,GSM7987448,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Ob-GR2_S6_R2_001.fastq.gz Ob-GR2_S6_R1_001.fastq.gz,fastq fastq,6044999600.0,15112499.0,GSM7987448 r1,0:200 1:200,A:1547731745;C:1388120378;G:1581574912;T:1523597213;N:3975352,200,200,,,1547731745,1388120378,1581574912,1523597213,3975352,SRX22985581,SRS19950789,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.36888,0.02272,0.01109,0.00038,0.86914,0.99328,0.46943,0.4982,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29192,SRR27308234,SRX22985580,SRS19950790,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP /sp7+  Osteoblast  rep1,GSM7987447,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP /sp7+  Osteoblast  rep1,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Osteoblasts|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987447,GSM7987447: EGFP /sp7+  Osteoblast  rep1; Danio rerio; RNA Seq,GSM7987447 r1,GSM7987447,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Ob-GR_S77_R1_001.fastq.gz Ob-GR_S77_R2_001.fastq.gz,fastq fastq,4847773600.0,12119434.0,GSM7987447 r1,0:200 1:200,A:1242312480;C:1120397684;G:1256425065;T:1226991694;N:1646677,200,200,,,1242312480,1120397684,1256425065,1226991694,1646677,SRX22985580,SRS19950790,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.0146,0.02559,0.00038,0.00052,0.99397,0.99405,0.50471,0.47146,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29193,SRR27308235,SRX22985579,SRS19950788,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP+/sp7+  OMP  rep2,GSM7987446,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP+/sp7+  OMP  rep2,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987446,GSM7987446: EGFP+/sp7+  OMP  rep2; Danio rerio; RNA Seq,GSM7987446 r1,GSM7987446,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Ob-G2_S5_R2_001.fastq.gz Ob-G2_S5_R1_001.fastq.gz,fastq fastq,6253558800.0,15633897.0,GSM7987446 r1,0:200 1:200,A:1638931864;C:1404420075;G:1600115132;T:1605939571;N:4152158,200,200,,,1638931864,1404420075,1600115132,1605939571,4152158,SRX22985579,SRS19950788,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.41021,0.02334,0.01523,0.00074,0.83989,0.99099,0.52255,0.52173,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29194,SRR27308236,SRX22985578,SRS19950791,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP+/sp7+  OMP  rep1,GSM7987445,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP+/sp7+  OMP  rep1,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Osteogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987445,GSM7987445: EGFP+/sp7+  OMP  rep1; Danio rerio; RNA Seq,GSM7987445 r1,GSM7987445,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Ob-G_S28_R2_001.fastq.gz Ob-G_S28_R1_001.fastq.gz,fastq fastq,4832320400.0,12080801.0,GSM7987445 r1,0:200 1:200,A:1252095509;C:1107971153;G:1236349772;T:1233319775;N:2584191,200,200,,,1252095509,1107971153,1236349772,1233319775,2584191,SRX22985578,SRS19950791,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01133,0.02895,0.00033,0.00043,0.99439,0.99297,0.50298,0.45574,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29195,SRR27308237,SRX22985577,SRS19950787,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP+/sp7   CMP  rep2,GSM7987444,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP+/sp7   CMP  rep2,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987444,GSM7987444: EGFP+/sp7   CMP  rep2; Danio rerio; RNA Seq,GSM7987444 r1,GSM7987444,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Mes-G2_S4_R1_001.fastq.gz Mes-G2_S4_R2_001.fastq.gz,fastq fastq,5812163600.0,14530409.0,GSM7987444 r1,0:200 1:200,A:1538664561;C:1291748975;G:1473028809;T:1504905134;N:3816121,200,200,,,1538664561,1291748975,1473028809,1504905134,3816121,SRX22985577,SRS19950787,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.40138,0.02482,0.0176,0.00091,0.83918,0.99099,0.47875,0.43124,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
29196,SRR27308238,SRX22985576,SRS19950786,SRP479308,PRJNA1055256,Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish,GSE251757,Transcriptome Analysis,Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development  growth  and homeostasis. However  developmental origins of osteoblasts and chondroblasts  lineage relationship  progenitor cells  and their differentiation potentials throughout animal life are not seamlessly understood. In this study  we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages  and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed  they never change their lineage identities throughout their lives  even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells  OPCs  which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin  we isolated sp7  mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs  chondrogenic mesenchymal progenitors CMPs  and osteoblasts.,,pubmed:38193362,,EGFP+/sp7   CMP  rep1,GSM7987443,,source name:14 dpa adult caudal fin|tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry|geo loc name:missing|collection date:missing,EGFP+/sp7   CMP  rep1,High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id  length  Genbank id  RNA type  gene name  product  raw count  RPKM and TPM values.,14 dpa adult caudal fin,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,tissue:14 dpa adult caudal fin|cell type:Chondrogenic mesenchymal progenitors|genotype:Tgcryaa:EGFP  sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry,GSM7987443,GSM7987443: EGFP+/sp7   CMP  rep1; Danio rerio; RNA Seq,GSM7987443 r1,GSM7987443,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP479308,,,Mes-G_S15_R1_001.fastq.gz Mes-G_S15_R2_001.fastq.gz,fastq fastq,5321588000.0,13303970.0,GSM7987443 r1,0:200 1:200,A:1405233304;C:1195662643;G:1342003810;T:1376732727;N:1955516,200,200,,,1405233304,1195662643,1342003810,1376732727,1955516,SRX22985576,SRS19950786,SRA1773396,"Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.00961,0.02419,0.00032,0.00052,0.9945,0.99324,0.51073,0.48429,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-12-20,Adult,Adult,Fin,Surface Structure
30628,SRR27942672,SRX23599456,SRS20442304,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,6 day post amputation replicate 2,6dpa fin2,,strain:Tgsp7:EGFP|age:1 year|collection date:2022 02 04|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:6 day post amputation replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,6dpa fin2 snRNA,6dpa2 RNA,6dpa2 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,6dpa2-GEX-lib1_S2_L001_R2_001.fastq.gz 6dpa2-GEX-lib1_S2_L001_R1_001.fastq.gz,fastq fastq,88818703262.0,498981479.0,6dpa2 GEX lib1 S2 L001 R1 001.fastq.gz,0:28 1:150,A:27051219358;C:18185699713;G:19496959258;T:24083822607;N:1002326,28,150,,,27051219358,18185699713,19496959258,24083822607,1002326,SRX23599456,SRS20442304,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02864,0.84751,0.01449,0.29092,0.98169,0.82014,0.39586,0.64356,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30629,SRR27942673,SRX23599455,SRS20442303,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,6 day post amputation replicate 1,6dpa fin1,,strain:Tgsp7:EGFP|age:1 year|collection date:2022 02 04|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:6 day post amputation replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,6dpa fin1 snRNA,6dpa1 RNA,6dpa1 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,6dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz 6dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz,fastq fastq,106483322870.0,598220915.0,6dpa1 GEX lib1 S1 L001 R1 001.fastq.gz,0:28 1:150,A:32833929738;C:22259209515;G:23233729505;T:28155235335;N:1218777,28,150,,,32833929738,22259209515,23233729505,28155235335,1218777,SRX23599455,SRS20442303,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02691,0.87324,0.01263,0.22013,0.98415,0.83144,0.4808,0.62463,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30630,SRR27942674,SRX23599454,SRS20442302,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,4 day post amputation replicate 2,4dpa fin2,,strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 12|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:4 day post amputation replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,4dpa fin2 snRNA,4dpa2 RNA,4dpa2 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,4dpa2-GEX-lib1_S2_L002_R1_001.fastq.gz 4dpa2-GEX-lib1_S2_L002_R2_001.fastq.gz,fastq fastq,100355045420.0,563792390.0,4dpa2 GEX lib1 S2 L002 R1 001.fastq.gz,0:28 1:150,A:30110360316;C:21497825420;G:22061747902;T:26684746811;N:364971,28,150,,,30110360316,21497825420,22061747902,26684746811,364971,SRX23599454,SRS20442302,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02956,0.90492,0.01391,0.21143,0.98324,0.82347,0.46993,0.73177,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30631,SRR27942675,SRX23599453,SRS20442301,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,4 day post amputation replicate 1,4dpa fin1,,strain:Tgsp7:EGFP|age:1 year|collection date:2021 11 22|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:4 day post amputation replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,4dpa fin1 snRNA,4dpa1 RNA,4dpa1 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,4dpa1-GEX-lib1_S1_L002_R2_001.fastq.gz 4dpa1-GEX-lib1_S1_L002_R1_001.fastq.gz,fastq fastq,104945766346.0,589582957.0,4dpa1 GEX lib1 S1 L002 R1 001.fastq.gz,0:28 1:150,A:32489394291;C:21756067815;G:22868928766;T:27829952922;N:1422552,28,150,,,32489394291,21756067815,22868928766,27829952922,1422552,SRX23599453,SRS20442301,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02921,0.86985,0.01399,0.22211,0.98372,0.8294,0.45783,0.71655,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30632,SRR27942676,SRX23599452,SRS20442300,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,2 day post amputation replicate 2,2dpa fin2,,strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 12|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:2 day post amputation replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,2dpa fin2 snRNA,2dpa2 RNA,2dpa2 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,2dpa2-GEX-lib1_S1_L001_R2_001.fastq.gz 2dpa2-GEX-lib1_S1_L001_R1_001.fastq.gz,fastq fastq,84977307334.0,477400603.0,2dpa2 GEX lib1 S1 L001 R1 001.fastq.gz,0:28 1:150,A:25498895454;C:18439149160;G:19015549944;T:22023275686;N:437090,28,150,,,25498895454,18439149160,19015549944,22023275686,437090,SRX23599452,SRS20442300,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02811,0.91493,0.01297,0.18571,0.98492,0.83554,0.4671,0.75085,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30633,SRR27942677,SRX23599451,SRS20442299,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,2 day post amputation replicate 1,2dpa fin1,,strain:Tgsp7:EGFP|age:1 year|collection date:2021 11 22|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:2 day post amputation replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,2dpa fin1 snRNA,2dpa1 RNA,2dpa1 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,2dpa1-GEX-lib1_S2_L002_R1_001.fastq.gz 2dpa1-GEX-lib1_S2_L002_R2_001.fastq.gz,fastq fastq,93046027220.0,522730490.0,2dpa1 GEX lib1 S2 L002 R1 001.fastq.gz,0:28 1:150,A:28562453325;C:19484276400;G:20294346104;T:24703683984;N:1267407,28,150,,,28562453325,19484276400,20294346104,24703683984,1267407,SRX23599451,SRS20442299,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.03074,0.88234,0.01398,0.22441,0.98405,0.83268,0.48065,0.74026,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30634,SRR27942678,SRX23599450,SRS20442298,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,1 day post amputation replicate 2,1dpa fin2,,strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 27|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:1 day post amputation replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,1dpa fin2 snRNA,1dpa2 RNA,1dpa2 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,1dpa2-GEX-lib1_S1_L004_R1_001.fastq.gz 1dpa2-GEX-lib1_S1_L004_R2_001.fastq.gz,fastq fastq,84562055050.0,475067725.0,1dpa2 GEX lib1 S1 L004 R1 001.fastq.gz,0:28 1:150,A:25830017026;C:17874013165;G:18722117096;T:22135719607;N:188156,28,150,,,25830017026,17874013165,18722117096,22135719607,188156,SRX23599450,SRS20442298,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02723,0.88745,0.01218,0.18561,0.98573,0.83613,0.45958,0.63016,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30635,SRR27942679,SRX23599449,SRS20442297,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,1 day post amputation replicate 1,1dpa fin1,,strain:Tgsp7:EGFP|age:1 year|collection date:2021 07 26|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:1 day post amputation replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,1dpa fin1 snRNA,1dpa1 RNA,1dpa1 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,1dpa1-GEX-lib1_S3_L002_R2_002.fastq.gz 1dpa1-GEX-lib1_S3_L002_R1_002.fastq.gz 1dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz 1dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz,fastq fastq fastq fastq,81494415866.0,457833797.0,1dpa1 GEX lib1 S1 L001 R1 001.fastq.gz,0:28 1:150,A:25109914971;C:16807439152;G:17406389176;T:22169842983;N:829584,28,150,,,25109914971,16807439152,17406389176,22169842983,829584,SRX23599449,SRS20442297,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02792,0.87908,0.0123,0.19441,0.98194,0.83644,0.4621,0.70445,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30636,SRR27942690,SRX23599438,SRS20442296,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,0 day post amputation replicate 2,0dpa fin2,,strain:Tgsp7:EGFP|age:1 year|collection date:2022 01 27|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:0 day post amputation replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,0dpa fin2 snRNA,0dpa2 RNA,0dpa2 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,0dpa2-GEX-lib1_S2_L004_R2_001.fastq.gz 0dpa2-GEX-lib1_S2_L004_R1_001.fastq.gz,fastq fastq,94016384252.0,528181934.0,0dpa2 GEX lib1 S2 L004 R1 001.fastq.gz,0:28 1:150,A:28851000041;C:19680536935;G:20640186670;T:24844451695;N:208911,28,150,,,28851000041,19680536935,20640186670,24844451695,208911,SRX23599438,SRS20442296,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02684,0.87686,0.01274,0.21544,0.98703,0.85975,0.45722,0.74164,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
30637,SRR27942691,SRX23599437,SRS20442295,SRP489317,PRJNA1075480,Common and Specific Gene Regulatory Programs in Zebrafish Caudal Fin Regeneration at Single Cell Resolution,PRJNA1075480,Other,Our goal is to delineate the transcriptomic and chromatin accessibility landscape across different cell types during the regeneration of the zebrafish caudal fin. Nuclei were isolated from caudal fin tissues at both pre injury and various stages of regeneration 1  2  4  and 6 dy post amputation  dpa for single nucleus multi omics sequencing paired snATAC seq and snRNA seq.,,pubmed:39809530,,0 day post amputation replicate 1,0dpa fin1,,strain:Tgsp7:EGFP|age:1 year|collection date:2021 07 26|geo loc name:not applicable|sex:not determined|tissue:Caudal fin|time point and replicate:0 day post amputation replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,0dpa fin1 snRNA,0dpa1 RNA,0dpa1 RNA,Cadual fin tissue  nuclei extraction  10x Genomics Chromium Single Cell Multiome,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP489317,,,0dpa1-GEX-lib1_S1_L001_R1_001.fastq.gz 0dpa1-GEX-lib1_S1_L001_R2_001.fastq.gz,fastq fastq,95106992388.0,534308946.0,0dpa1 GEX lib1 S1 L001 R1 001.fastq.gz,0:28 1:150,A:29570202174;C:19531427210;G:20167731244;T:25836092390;N:1539370,28,150,,,29570202174,19531427210,20167731244,25836092390,1539370,SRX23599437,SRS20442295,SRA1801018,Washington University in St. Louis School of Medicine|Genetics,Washington University in St. Louis School of Medicine,2,0.02388,0.87039,0.01162,0.24031,0.98652,0.85354,0.48963,0.74378,28,150,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-02-12,Adult,Adult,Fin,Surface Structure
33837,SRR30763634,SRX26165999,SRS22710780,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin con2,Skin con 3,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 3|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin con 3,SK CON 3,SK CON 3,Zebrafish skin at control group,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_con2_Clean_Data1.fq.gz Skin_con2_Clean_Data2.fq.gz,fastq fastq,6083362246.0,21717347.0,Skin con2 Clean Data1.fq.gz,0:140.06 1:140.05,A:1575684711;C:1458969719;G:1469933956;T:1578641539;N:132321,140,140,,,1575684711,1458969719,1469933956,1578641539,132321,SRX26165999,SRS22710780,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
33838,SRR30763635,SRX26165998,SRS22710779,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin con1,Skin con 2,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 2|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin con 2,SK CON 2,SK CON 2,Zebrafish skin at control group,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_con1_Clean_Data1.fq.gz Skin_con1_Clean_Data2.fq.gz,fastq fastq,5776524166.0,20610041.0,Skin con1 Clean Data1.fq.gz,0:140.14 1:140.13,A:1496887200;C:1385008310;G:1395131090;T:1499373290;N:124276,140,140,,,1496887200,1385008310,1395131090,1499373290,124276,SRX26165998,SRS22710779,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
33839,SRR30763636,SRX26165997,SRS22710778,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin con,Skin con 1,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 1|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin con 1,SK CON 1,SK CON 1,Zebrafish skin at control group,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_con_Clean_Data1.fq.gz Skin_con_Clean_Data2.fq.gz,fastq fastq,5304184337.0,18925504.0,Skin con Clean Data1.fq.gz,0:140.14 1:140.13,A:1400015654;C:1245459230;G:1267684230;T:1391013551;N:11672,140,140,,,1400015654,1245459230,1267684230,1391013551,11672,SRX26165997,SRS22710778,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
33840,SRR30763637,SRX26165996,SRS22710777,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin 3dpi2,Skin 3d 3,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 3|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin 3d 3,SK 3D 3,SK 3D 3,Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_3dpi2_Clean_Data1.fq.gz Skin_3dpi2_Clean_Data2.fq.gz,fastq fastq,5528962547.0,19717071.0,Skin 3dpi2 Clean Data1.fq.gz,0:140.21 1:140.20,A:1434889776;C:1319598036;G:1335801562;T:1438550030;N:123143,140,140,,,1434889776,1319598036,1335801562,1438550030,123143,SRX26165996,SRS22710777,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
33841,SRR30763638,SRX26165995,SRS22710776,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin 3dpi1,Skin 3d 2,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 2|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin 3d 2,SK 3D 2,SK 3D 2,Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_3dpi1_Clean_Data1.fq.gz Skin_3dpi1_Clean_Data2.fq.gz,fastq fastq,6045424568.0,21559158.0,Skin 3dpi1 Clean Data1.fq.gz,0:140.21 1:140.20,A:1566211023;C:1442845401;G:1464489674;T:1571745680;N:132790,140,140,,,1566211023,1442845401,1464489674,1571745680,132790,SRX26165995,SRS22710776,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
33842,SRR30763639,SRX26165994,SRS22710775,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin 3dpi,Skin 3d 1,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 1|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin 3d 1,SK 3D 1,SK 3D 1,Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_3dpi_Clean_Data1.fq.gz Skin_3dpi_Clean_Data2.fq.gz,fastq fastq,5398897838.0,19388025.0,Skin 3dpi Clean Data1.fq.gz,0:139.24 1:139.23,A:1434301676;C:1260747084;G:1277759027;T:1426077485;N:12566,139,139,,,1434301676,1260747084,1277759027,1426077485,12566,SRX26165994,SRS22710775,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
33843,SRR30763640,SRX26165993,SRS22710774,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin 1dpi2,Skin 1d 3,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 3|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin 1d 3,SK 1D 3,SK 1D 3,Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_1dpi2_Clean_Data1.fq.gz Skin_1dpi2_Clean_Data2.fq.gz,fastq fastq,6317753535.0,22527726.0,Skin 1dpi2 Clean Data1.fq.gz,0:140.23 1:140.22,A:1637469629;C:1508203339;G:1526532646;T:1645411954;N:135967,140,140,,,1637469629,1508203339,1526532646,1645411954,135967,SRX26165993,SRS22710774,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
33844,SRR30763641,SRX26165992,SRS22710773,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin 1dpi1,Skin 1d 2,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 2|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin 1d 2,SK 1D 2,SK 1D 2,Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_1dpi1_Clean_Data1.fq.gz Skin_1dpi1_Clean_Data2.fq.gz,fastq fastq,5665401221.0,20209478.0,Skin 1dpi1 Clean Data1.fq.gz,0:140.17 1:140.16,A:1463485728;C:1359900876;G:1372085350;T:1469804976;N:124291,140,140,,,1463485728,1359900876,1372085350,1469804976,124291,SRX26165992,SRS22710773,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
33845,SRR30763642,SRX26165991,SRS22710772,SRP534093,PRJNA1163532,Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus,PRJNA1163532,Whole Genome Sequencing,,,,,Skin 1dpi,Skin 1d 1,,breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 1|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish skin   RNA seq  Skin 1d 1,SK 1D 1,SK 1D 1,Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP534093,,,Skin_1dpi_Clean_Data1.fq.gz Skin_1dpi_Clean_Data2.fq.gz,fastq fastq,4758945020.0,17104843.0,Skin 1dpi Clean Data1.fq.gz,0:139.12 1:139.11,A:1261511064;C:1113177324;G:1128285977;T:1255959998;N:10657,139,139,,,1261511064,1113177324,1128285977,1255959998,10657,SRX26165991,SRS22710772,SRA1977051,Northwest A&amp;F University|College of Animal Science and Technology,Northwest A&F University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-09-22,Adult,Adult,Skin,Surface Structure
34294,SRR31642040,SRX27005496,SRS23470018,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  70 dpjr  Single,GSM8671781,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  70 dpjr  Single,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2,GSM8671781,GSM8671781: Jaw joint cells  70 dpjr  Single; Danio rerio; RNA Seq,GSM8671781 r1,GSM8671781,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,70dpjr_Single_Animal_L002_I1_001.fastq.gz 70dpjr_Single_Animal_L002_I2_001.fastq.gz 70dpjr_Single_Animal_L002_R1_001.fastq.gz 70dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,37049181954.0,166888207.0,GSM8671781 r1,0:10 1:10 2:101 3:101,A:9816927833;C:6602658028;G:6479430305;T:10811804702;N:596946,10,10,101,101,9816927833,6602658028,6479430305,10811804702,596946,SRX27005496,SRS23470018,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34295,SRR31642041,SRX27005496,SRS23470018,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  70 dpjr  Single,GSM8671781,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  70 dpjr  Single,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2,GSM8671781,GSM8671781: Jaw joint cells  70 dpjr  Single; Danio rerio; RNA Seq,GSM8671781 r1,GSM8671781,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,70dpjr_Single_Animal_L003_I1_001.fastq.gz 70dpjr_Single_Animal_L003_I2_001.fastq.gz 70dpjr_Single_Animal_L003_R1_001.fastq.gz 70dpjr_Single_Animal_L003_R2_001.fastq.gz,fastq fastq fastq fastq,37422563532.0,168570106.0,GSM8671781 r2,0:10 1:10 2:101 3:101,A:9984119286;C:6706845163;G:6549173156;T:10810402697;N:621110,10,10,101,101,9984119286,6706845163,6549173156,10810402697,621110,SRX27005496,SRS23470018,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34296,SRR31642042,SRX27005495,SRS23470017,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  70 dpjr  Pooled,GSM8671780,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  70 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2,GSM8671780,GSM8671780: Jaw joint cells  70 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671780 r1,GSM8671780,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,70dpjr_Pooled_L002_I1_001.fastq.gz 70dpjr_Pooled_L002_I2_001.fastq.gz 70dpjr_Pooled_L002_R1_001.fastq.gz 70dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,38777301438.0,174672529.0,GSM8671780 r1,0:10 1:10 2:101 3:101,A:10225368778;C:6854296513;G:6738650656;T:11464913181;N:621730,10,10,101,101,10225368778,6854296513,6738650656,11464913181,621730,SRX27005495,SRS23470017,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34297,SRR31642043,SRX27005495,SRS23470017,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  70 dpjr  Pooled,GSM8671780,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  70 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:70 dpjr|batch:2,GSM8671780,GSM8671780: Jaw joint cells  70 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671780 r1,GSM8671780,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,70dpjr_Pooled_L003_I1_001.fastq.gz 70dpjr_Pooled_L003_I2_001.fastq.gz 70dpjr_Pooled_L003_R1_001.fastq.gz 70dpjr_Pooled_L003_R2_001.fastq.gz,fastq fastq fastq fastq,39504660018.0,177948919.0,GSM8671780 r2,0:10 1:10 2:101 3:101,A:10484112013;C:7025634996;G:6867358428;T:11567917628;N:658573,10,10,101,101,10484112013,7025634996,6867358428,11567917628,658573,SRX27005495,SRS23470017,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34298,SRR31642044,SRX27005494,SRS23470016,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  28 dpjr  Single Animal,GSM8671779,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  28 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2,GSM8671779,GSM8671779: Jaw joint cells  28 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671779 r1,GSM8671779,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,28dpjr_Single_Animal_L002_I1_001.fastq.gz 28dpjr_Single_Animal_L002_I2_001.fastq.gz 28dpjr_Single_Animal_L002_R1_001.fastq.gz 28dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,36462195750.0,164244125.0,GSM8671779 r1,0:10 1:10 2:101 3:101,A:9480759740;C:6602174265;G:6480198740;T:10613598349;N:582156,10,10,101,101,9480759740,6602174265,6480198740,10613598349,582156,SRX27005494,SRS23470016,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34299,SRR31642045,SRX27005494,SRS23470016,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  28 dpjr  Single Animal,GSM8671779,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  28 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2,GSM8671779,GSM8671779: Jaw joint cells  28 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671779 r1,GSM8671779,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,28dpjr_Single_Animal_L003_I1_001.fastq.gz 28dpjr_Single_Animal_L003_I2_001.fastq.gz 28dpjr_Single_Animal_L003_R1_001.fastq.gz 28dpjr_Single_Animal_L003_R2_001.fastq.gz,fastq fastq fastq fastq,37308768774.0,168057517.0,GSM8671779 r2,0:10 1:10 2:101 3:101,A:9765937139;C:6796393106;G:6628239898;T:10756427871;N:620420,10,10,101,101,9765937139,6796393106,6628239898,10756427871,620420,SRX27005494,SRS23470016,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34300,SRR31642046,SRX27005493,SRS23470015,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  28 dpjr  Pooled,GSM8671778,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  28 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2,GSM8671778,GSM8671778: Jaw joint cells  28 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671778 r1,GSM8671778,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,28dpjr_Pooled_L002_I1_001.fastq.gz 28dpjr_Pooled_L002_I2_001.fastq.gz 28dpjr_Pooled_L002_R1_001.fastq.gz 28dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,37406314908.0,168496914.0,GSM8671778 r1,0:10 1:10 2:101 3:101,A:9851624515;C:6742015789;G:6561704544;T:10880437218;N:594562,10,10,101,101,9851624515,6742015789,6561704544,10880437218,594562,SRX27005493,SRS23470015,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34301,SRR31642047,SRX27005493,SRS23470015,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  28 dpjr  Pooled,GSM8671778,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  28 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2,GSM8671778,GSM8671778: Jaw joint cells  28 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671778 r1,GSM8671778,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,28dpjr_Pooled_L003_I1_001.fastq.gz 28dpjr_Pooled_L003_I2_001.fastq.gz 28dpjr_Pooled_L003_R1_001.fastq.gz 28dpjr_Pooled_L003_R2_001.fastq.gz,fastq fastq fastq fastq,38288256750.0,172469625.0,GSM8671778 r2,0:10 1:10 2:101 3:101,A:10150332803;C:6940223173;G:6717128076;T:11030541750;N:638448,10,10,101,101,10150332803,6940223173,6717128076,11030541750,638448,SRX27005493,SRS23470015,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34302,SRR31642048,SRX27005492,SRS23470014,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  14 dpjr  Single Animal,GSM8671777,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  14 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2,GSM8671777,GSM8671777: Jaw joint cells  14 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671777 r1,GSM8671777,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,14dpjr_Single_Animal_L002_I1_001.fastq.gz 14dpjr_Single_Animal_L002_I2_001.fastq.gz 14dpjr_Single_Animal_L002_R1_001.fastq.gz 14dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,37035287196.0,166825618.0,GSM8671777 r1,0:10 1:10 2:101 3:101,A:9648639338;C:6931863960;G:6677103016;T:10440574408;N:594114,10,10,101,101,9648639338,6931863960,6677103016,10440574408,594114,SRX27005492,SRS23470014,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34303,SRR31642049,SRX27005492,SRS23470014,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  14 dpjr  Single Animal,GSM8671777,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  14 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2,GSM8671777,GSM8671777: Jaw joint cells  14 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671777 r1,GSM8671777,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,14dpjr_Single_Animal_L003_I1_001.fastq.gz 14dpjr_Single_Animal_L003_I2_001.fastq.gz 14dpjr_Single_Animal_L003_R1_001.fastq.gz 14dpjr_Single_Animal_L003_R2_001.fastq.gz,fastq fastq fastq fastq,37643417790.0,169564945.0,GSM8671777 r2,0:10 1:10 2:101 3:101,A:9871564441;C:7084478503;G:6791319850;T:10504128919;N:627177,10,10,101,101,9871564441,7084478503,6791319850,10504128919,627177,SRX27005492,SRS23470014,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34304,SRR31642050,SRX27005491,SRS23470013,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  14 dpjr  Pooled,GSM8671776,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  14 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2,GSM8671776,GSM8671776: Jaw joint cells  14 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671776 r1,GSM8671776,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,14dpjr_Pooled_L002_I1_001.fastq.gz 14dpjr_Pooled_L002_I2_001.fastq.gz 14dpjr_Pooled_L002_R1_001.fastq.gz 14dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,36987619800.0,166610900.0,GSM8671776 r1,0:10 1:10 2:101 3:101,A:9731052223;C:6612084734;G:6474066275;T:10837609042;N:589526,10,10,101,101,9731052223,6612084734,6474066275,10837609042,589526,SRX27005491,SRS23470013,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34305,SRR31642051,SRX27005491,SRS23470013,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  14 dpjr  Pooled,GSM8671776,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  14 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2,GSM8671776,GSM8671776: Jaw joint cells  14 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671776 r1,GSM8671776,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,14dpjr_Pooled_L003_I1_001.fastq.gz 14dpjr_Pooled_L003_I2_001.fastq.gz 14dpjr_Pooled_L003_R1_001.fastq.gz 14dpjr_Pooled_L003_R2_001.fastq.gz,fastq fastq fastq fastq,37823124792.0,170374436.0,GSM8671776 r2,0:10 1:10 2:101 3:101,A:10018290148;C:6801679608;G:6619700517;T:10975336592;N:629207,10,10,101,101,10018290148,6801679608,6619700517,10975336592,629207,SRX27005491,SRS23470013,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34306,SRR31642052,SRX27005490,SRS23470012,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  7 dpjr  Single Animal,GSM8671775,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  7 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1,GSM8671775,GSM8671775: Jaw joint cells  7 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671775 r1,GSM8671775,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,7dpjr_Single_Animal_L001_I1_001.fastq.gz 7dpjr_Single_Animal_L001_I2_001.fastq.gz 7dpjr_Single_Animal_L001_R1_001.fastq.gz 7dpjr_Single_Animal_L001_R2_001.fastq.gz,fastq fastq fastq fastq,40902096516.0,184243678.0,GSM8671775 r1,0:10 1:10 2:101 3:101,A:9783975092;C:6823114397;G:6613251892;T:13996577499;N:304076,10,10,101,101,9783975092,6823114397,6613251892,13996577499,304076,SRX27005490,SRS23470012,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34307,SRR31642053,SRX27005490,SRS23470012,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  7 dpjr  Single Animal,GSM8671775,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  7 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1,GSM8671775,GSM8671775: Jaw joint cells  7 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671775 r1,GSM8671775,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,7dpjr_Single_Animal_L002_I1_001.fastq.gz 7dpjr_Single_Animal_L002_I2_001.fastq.gz 7dpjr_Single_Animal_L002_R1_001.fastq.gz 7dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,41355254682.0,186284931.0,GSM8671775 r2,0:10 1:10 2:101 3:101,A:9943607268;C:6874125553;G:6628853095;T:14182629385;N:340761,10,10,101,101,9943607268,6874125553,6628853095,14182629385,340761,SRX27005490,SRS23470012,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34308,SRR31642054,SRX27005489,SRS23470011,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  7 dpjr  Pooled,GSM8671774,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  7 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1,GSM8671774,GSM8671774: Jaw joint cells  7 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671774 r1,GSM8671774,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,7dpjr_Pooled_L001_I1_001.fastq.gz 7dpjr_Pooled_L001_I2_001.fastq.gz 7dpjr_Pooled_L001_R1_001.fastq.gz 7dpjr_Pooled_L001_R2_001.fastq.gz,fastq fastq fastq fastq,53197411338.0,239627979.0,GSM8671774 r1,0:10 1:10 2:101 3:101,A:12697683552;C:8693291955;G:8466190901;T:18547291431;N:393919,10,10,101,101,12697683552,8693291955,8466190901,18547291431,393919,SRX27005489,SRS23470011,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34309,SRR31642055,SRX27005489,SRS23470011,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  7 dpjr  Pooled,GSM8671774,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  7 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1,GSM8671774,GSM8671774: Jaw joint cells  7 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671774 r1,GSM8671774,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,7dpjr_Pooled_L002_I1_001.fastq.gz 7dpjr_Pooled_L002_I2_001.fastq.gz 7dpjr_Pooled_L002_R1_001.fastq.gz 7dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,53485697430.0,240926565.0,GSM8671774 r2,0:10 1:10 2:101 3:101,A:12829769456;C:8708244775;G:8441746450;T:18686966286;N:439163,10,10,101,101,12829769456,8708244775,8441746450,18686966286,439163,SRX27005489,SRS23470011,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34310,SRR31642056,SRX27005488,SRS23470010,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  3 dpjr  Single Animal,GSM8671773,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  3 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1,GSM8671773,GSM8671773: Jaw joint cells  3 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671773 r1,GSM8671773,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,3dpjr_Single_Animal_L001_I1_001.fastq.gz 3dpjr_Single_Animal_L001_I2_001.fastq.gz 3dpjr_Single_Animal_L001_R1_001.fastq.gz 3dpjr_Single_Animal_L001_R2_001.fastq.gz,fastq fastq fastq fastq,49273120002.0,221950991.0,GSM8671773 r1,0:10 1:10 2:101 3:101,A:11736989822;C:8276159891;G:8014521470;T:16806059958;N:369041,10,10,101,101,11736989822,8276159891,8014521470,16806059958,369041,SRX27005488,SRS23470010,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34311,SRR31642057,SRX27005488,SRS23470010,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  3 dpjr  Single Animal,GSM8671773,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  3 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1,GSM8671773,GSM8671773: Jaw joint cells  3 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671773 r1,GSM8671773,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,3dpjr_Single_Animal_L002_I1_001.fastq.gz 3dpjr_Single_Animal_L002_I2_001.fastq.gz 3dpjr_Single_Animal_L002_R1_001.fastq.gz 3dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,49592342904.0,223388932.0,GSM8671773 r2,0:10 1:10 2:101 3:101,A:11873700952;C:8297783357;G:7995460477;T:16957208840;N:410638,10,10,101,101,11873700952,8297783357,7995460477,16957208840,410638,SRX27005488,SRS23470010,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34312,SRR31642058,SRX27005487,SRS23470009,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  3 dpjr  Pooled,GSM8671772,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  3 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1,GSM8671772,GSM8671772: Jaw joint cells  3 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671772 r1,GSM8671772,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,3dpjr_Pooled_L001_I1_001.fastq.gz 3dpjr_Pooled_L001_I2_001.fastq.gz 3dpjr_Pooled_L001_R1_001.fastq.gz 3dpjr_Pooled_L001_R2_001.fastq.gz,fastq fastq fastq fastq,44552263362.0,200685871.0,GSM8671772 r1,0:10 1:10 2:101 3:101,A:10490408187;C:7710053398;G:7420808306;T:14916942634;N:333417,10,10,101,101,10490408187,7710053398,7420808306,14916942634,333417,SRX27005487,SRS23470009,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34313,SRR31642059,SRX27005487,SRS23470009,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  3 dpjr  Pooled,GSM8671772,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  3 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1,GSM8671772,GSM8671772: Jaw joint cells  3 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671772 r1,GSM8671772,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,3dpjr_Pooled_L002_I1_001.fastq.gz 3dpjr_Pooled_L002_I2_001.fastq.gz 3dpjr_Pooled_L002_R1_001.fastq.gz 3dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,44828540142.0,201930361.0,GSM8671772 r2,0:10 1:10 2:101 3:101,A:10609297758;C:7728774755;G:7401748035;T:15049741661;N:370713,10,10,101,101,10609297758,7728774755,7401748035,15049741661,370713,SRX27005487,SRS23470009,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34314,SRR31642060,SRX27005486,SRS23470008,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  1 dpjr  Single Animal,GSM8671771,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  1 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1,GSM8671771,GSM8671771: Jaw joint cells  1 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671771 r1,GSM8671771,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,1dpjr_Single_Animal_L001_I1_001.fastq.gz 1dpjr_Single_Animal_L001_I2_001.fastq.gz 1dpjr_Single_Animal_L001_R1_001.fastq.gz 1dpjr_Single_Animal_L001_R2_001.fastq.gz,fastq fastq fastq fastq,42674862642.0,192229111.0,GSM8671771 r1,0:10 1:10 2:101 3:101,A:10158179078;C:7131592111;G:6936536781;T:14603653251;N:319201,10,10,101,101,10158179078,7131592111,6936536781,14603653251,319201,SRX27005486,SRS23470008,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34315,SRR31642061,SRX27005486,SRS23470008,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  1 dpjr  Single Animal,GSM8671771,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  1 dpjr  Single Animal,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1,GSM8671771,GSM8671771: Jaw joint cells  1 dpjr  Single Animal; Danio rerio; RNA Seq,GSM8671771 r1,GSM8671771,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,1dpjr_Single_Animal_L002_I1_001.fastq.gz 1dpjr_Single_Animal_L002_I2_001.fastq.gz 1dpjr_Single_Animal_L002_R1_001.fastq.gz 1dpjr_Single_Animal_L002_R2_001.fastq.gz,fastq fastq fastq fastq,42871754220.0,193116010.0,GSM8671771 r2,0:10 1:10 2:101 3:101,A:10257131897;C:7136718897;G:6908261223;T:14706965739;N:356264,10,10,101,101,10257131897,7136718897,6908261223,14706965739,356264,SRX27005486,SRS23470008,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34316,SRR31642062,SRX27005485,SRS23470007,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  1 dpjr  Pooled,GSM8671770,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  1 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1,GSM8671770,GSM8671770: Jaw joint cells  1 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671770 r1,GSM8671770,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,1dpjr_Pooled_L001_I1_001.fastq.gz 1dpjr_Pooled_L001_I2_001.fastq.gz 1dpjr_Pooled_L001_R1_001.fastq.gz 1dpjr_Pooled_L001_R2_001.fastq.gz,fastq fastq fastq fastq,42118392336.0,189722488.0,GSM8671770 r1,0:10 1:10 2:101 3:101,A:10107137753;C:6968180312;G:6833097097;T:14415214595;N:312819,10,10,101,101,10107137753,6968180312,6833097097,14415214595,312819,SRX27005485,SRS23470007,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34317,SRR31642063,SRX27005485,SRS23470007,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  1 dpjr  Pooled,GSM8671770,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  1 dpjr  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1,GSM8671770,GSM8671770: Jaw joint cells  1 dpjr  Pooled; Danio rerio; RNA Seq,GSM8671770 r1,GSM8671770,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,1dpjr_Pooled_L002_I1_001.fastq.gz 1dpjr_Pooled_L002_I2_001.fastq.gz 1dpjr_Pooled_L002_R1_001.fastq.gz 1dpjr_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,42373992258.0,190873839.0,GSM8671770 r2,0:10 1:10 2:101 3:101,A:10221244303;C:6981947133;G:6814497183;T:14538473757;N:353102,10,10,101,101,10221244303,6981947133,6814497183,14538473757,353102,SRX27005485,SRS23470007,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34318,SRR31642064,SRX27005484,SRS23470006,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Single Animal 2,GSM8671769,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Single Animal 2,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2,GSM8671769,GSM8671769: Jaw joint cells  Uninjured  Single Animal 2; Danio rerio; RNA Seq,GSM8671769 r1,GSM8671769,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Single_Animal_2_L001_I1_001.fastq.gz Uninjured_Single_Animal_2_L001_I2_001.fastq.gz Uninjured_Single_Animal_2_L001_R1_001.fastq.gz Uninjured_Single_Animal_2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,44002559172.0,198209726.0,GSM8671769 r1,0:10 1:10 2:101 3:101,A:10399936361;C:7407718592;G:7226570159;T:15003813457;N:326083,10,10,101,101,10399936361,7407718592,7226570159,15003813457,326083,SRX27005484,SRS23470006,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34319,SRR31642065,SRX27005484,SRS23470006,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Single Animal 2,GSM8671769,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Single Animal 2,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2,GSM8671769,GSM8671769: Jaw joint cells  Uninjured  Single Animal 2; Danio rerio; RNA Seq,GSM8671769 r1,GSM8671769,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Single_Animal_2_L002_I1_001.fastq.gz Uninjured_Single_Animal_2_L002_I2_001.fastq.gz Uninjured_Single_Animal_2_L002_R1_001.fastq.gz Uninjured_Single_Animal_2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,44326343508.0,199668214.0,GSM8671769 r2,0:10 1:10 2:101 3:101,A:10528879457;C:7433951690;G:7216222556;T:15153558176;N:367349,10,10,101,101,10528879457,7433951690,7216222556,15153558176,367349,SRX27005484,SRS23470006,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34320,SRR31642066,SRX27005483,SRS23470005,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Single Animal 1,GSM8671768,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Single Animal 1,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1,GSM8671768,GSM8671768: Jaw joint cells  Uninjured  Single Animal 1; Danio rerio; RNA Seq,GSM8671768 r1,GSM8671768,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Single_Animal_1_L002_I1_001.fastq.gz Uninjured_Single_Animal_1_L002_I2_001.fastq.gz Uninjured_Single_Animal_1_L002_R1_001.fastq.gz Uninjured_Single_Animal_1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,42273543918.0,190421369.0,GSM8671768 r1,0:10 1:10 2:101 3:101,A:10987118484;C:7700883520;G:7585109100;T:12191335494;N:669940,10,10,101,101,10987118484,7700883520,7585109100,12191335494,669940,SRX27005483,SRS23470005,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34321,SRR31642067,SRX27005483,SRS23470005,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Single Animal 1,GSM8671768,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Single Animal 1,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1,GSM8671768,GSM8671768: Jaw joint cells  Uninjured  Single Animal 1; Danio rerio; RNA Seq,GSM8671768 r1,GSM8671768,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Single_Animal_1_L003_I1_001.fastq.gz Uninjured_Single_Animal_1_L003_I2_001.fastq.gz Uninjured_Single_Animal_1_L003_R1_001.fastq.gz Uninjured_Single_Animal_1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,43210917384.0,194643772.0,GSM8671768 r2,0:10 1:10 2:101 3:101,A:11303072754;C:7914534277;G:7759329632;T:12340392808;N:712473,10,10,101,101,11303072754,7914534277,7759329632,12340392808,712473,SRX27005483,SRS23470005,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34322,SRR31642068,SRX27005482,SRS23470004,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Pooled,GSM8671767,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2,GSM8671767,GSM8671767: Jaw joint cells  Uninjured  Pooled; Danio rerio; RNA Seq,GSM8671767 r1,GSM8671767,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Pooled_L001_I1_001.fastq.gz Uninjured_Pooled_L001_I2_001.fastq.gz Uninjured_Pooled_L001_R1_001.fastq.gz Uninjured_Pooled_L001_R2_001.fastq.gz,fastq fastq fastq fastq,44953034856.0,202491148.0,GSM8671767 r1,0:10 1:10 2:101 3:101,A:10830949570;C:7341800999;G:7101623323;T:15628500376;N:337628,10,10,101,101,10830949570,7341800999,7101623323,15628500376,337628,SRX27005482,SRS23470004,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,Surface Structure
34323,SRR31642069,SRX27005482,SRS23470004,SRP550052,PRJNA1195551,scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint,GSE283763,Transcriptome Analysis,Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.,,,,Jaw joint cells  Uninjured  Pooled,GSM8671767,,source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing,Jaw joint cells  Uninjured  Pooled,CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files,Jaw joint,Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer’s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2,GSM8671767,GSM8671767: Jaw joint cells  Uninjured  Pooled; Danio rerio; RNA Seq,GSM8671767 r1,GSM8671767,1,Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550052,,loader:fastq load.py,Uninjured_Pooled_L002_I1_001.fastq.gz Uninjured_Pooled_L002_I2_001.fastq.gz Uninjured_Pooled_L002_R1_001.fastq.gz Uninjured_Pooled_L002_R2_001.fastq.gz,fastq fastq fastq fastq,45169152966.0,203464653.0,GSM8671767 r2,0:10 1:10 2:101 3:101,A:10937981456;C:7348369082;G:7073920761;T:15739215927;N:372680,10,10,101,101,10937981456,7348369082,7073920761,15739215927,372680,SRX27005482,SRS23470004,SRA2029585,"Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center","Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-08,Adult,Adult,Jaw,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