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
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
76470,SRR24976460,SRX20733648,SRS18024487,SRP445049,PRJNA985650,Ancient vertebrate dermal armor evolved from trunk neural crest,GSE235280,Other,Bone is an evolutionary novelty of vertebrates  likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor  we have performed in vivo lineage tracing in the sterlet sturgeon  a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally  histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone  dentin and hypermineralized covering tissues  in various combinations  that resemble those of the first armored vertebrates. Taken together  our results support a primitive skeletogenic role for the neural crest along the entire body axis  that was later progressively restricted to the cranial region during vertebrate evolution. Thus  the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor  we performed bulk RNA sequencing of sterlet sturgeon scutes  scales of the Senegal bichir  and zebrafish scales.,,pubmed:37459514,,Zebrafish scale 30mm  replicate 2,GSM7498272,,source name:cells of elasmoid scale|tissue:cells of elasmoid scale|genotype:WT|measure:30 mm|geo loc name:missing|collection date:missing,Zebrafish scale 30mm  replicate 2,In brief  every sterlet/bichir protein sequence was queried locally against the zebrafish proteome  following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach  proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences  while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference  we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al.  2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample,cells of elasmoid scale,,RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.,,tissue:cells of elasmoid scale|genotype:WT|measure:30 mm,GSM7498272,GSM7498272: Zebrafish scale 30mm  replicate 2; Danio rerio; RNA Seq,GSM7498272 r1,GSM7498272,1,RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP445049,,,DR_scale_2.fastq.gz,fastq,3233423900.0,64668478.0,GSM7498272 r1,0:50,A:867694073;C:728518022;G:750424718;T:885367521;N:1419566,50,,,,867694073,728518022,750424718,885367521,1419566,SRX20733648,SRS18024487,SRA1659604,"Bronner, California Institute of Technology","Bronner, California Institute of Technology",1,0.89607,,0.08896,,0.72612,,0.4695,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-06-20,Undetermined,Undetermined,Scale,Surface Structure
76471,SRR24976461,SRX20733647,SRS18024486,SRP445049,PRJNA985650,Ancient vertebrate dermal armor evolved from trunk neural crest,GSE235280,Other,Bone is an evolutionary novelty of vertebrates  likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor  we have performed in vivo lineage tracing in the sterlet sturgeon  a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally  histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone  dentin and hypermineralized covering tissues  in various combinations  that resemble those of the first armored vertebrates. Taken together  our results support a primitive skeletogenic role for the neural crest along the entire body axis  that was later progressively restricted to the cranial region during vertebrate evolution. Thus  the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor  we performed bulk RNA sequencing of sterlet sturgeon scutes  scales of the Senegal bichir  and zebrafish scales.,,pubmed:37459514,,Zebrafish scale 30mm  replicate 1,GSM7498271,,source name:cells of elasmoid scale|tissue:cells of elasmoid scale|genotype:WT|measure:30 mm|geo loc name:missing|collection date:missing,Zebrafish scale 30mm  replicate 1,In brief  every sterlet/bichir protein sequence was queried locally against the zebrafish proteome  following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach  proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences  while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference  we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al.  2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample,cells of elasmoid scale,,RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.,,tissue:cells of elasmoid scale|genotype:WT|measure:30 mm,GSM7498271,GSM7498271: Zebrafish scale 30mm  replicate 1; Danio rerio; RNA Seq,GSM7498271 r1,GSM7498271,1,RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP445049,,,DR_scale_1.fastq.gz,fastq,2847639400.0,56952788.0,GSM7498271 r1,0:50,A:764903871;C:640842328;G:660536366;T:780092458;N:1264377,50,,,,764903871,640842328,660536366,780092458,1264377,SRX20733647,SRS18024486,SRA1659604,"Bronner, California Institute of Technology","Bronner, California Institute of Technology",1,0.89576,,0.08353,,0.73594,,0.45703,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-06-20,Undetermined,Undetermined,Scale,Surface Structure