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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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 123893447, 111981365, 116049412, 150953220, 20602, "ERX4862316", "ERS4959147", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.90777, null, 0.11921, null, 0.7137, null, 0.48182, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "ena EXPERIMENT BRISTOL 08 01 2021 15:14:53:482 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "DNase", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "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, null, null, 121063841, 109534722, 113610951, 147602721, 53899, "ERX4862315", "ERS4959147", "ERA3206662", "University of Bristol|European Nucleotide Archive", "University of Bristol", 1, 0.907, null, 0.11935, null, 0.71364, null, 0.48543, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "dnase", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-08-20", "Adult", "Adult", "Scale", "Surface Structure"], [28893, "SRR26821448", "SRX22518177", "SRS19529846", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "10mT fractured 3", "GSM7898626", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing", "10mT fractured 3", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs", "GSM7898626", "GSM7898626: 10mT fractured 3; Danio rerio; RNA Seq", "GSM7898626 r1", "GSM7898626", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "10mT_fractured_3_R2.fq.gz 10mT_fractured_3_R1.fq.gz", "fastq fastq", 1301482800.0, 4338276.0, "GSM7898626 r1", "0:150 1:150", "A:335087662;C:232566321;G:385245929;T:348358361;N:224527", 150, 150, null, null, 335087662, 232566321, 385245929, 348358361, 224527, "SRX22518177", "SRS19529846", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.67547, 0.04621, 0.23296, 0.03359, 0.78279, 0.99648, 0.54124, 0.52153, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [28894, "SRR26821449", "SRX22518176", "SRS19529845", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "10mT fractured 2", "GSM7898625", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing", "10mT fractured 2", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs", "GSM7898625", "GSM7898625: 10mT fractured 2; Danio rerio; RNA Seq", "GSM7898625 r1", "GSM7898625", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "10mT_fractured_2_R1.fq.gz 10mT_fractured_2_R2.fq.gz", "fastq fastq", 1507967100.0, 5026557.0, "GSM7898625 r1", "0:150 1:150", "A:390969189;C:278659472;G:444481407;T:393553558;N:303474", 150, 150, null, null, 390969189, 278659472, 444481407, 393553558, 303474, "SRX22518176", "SRS19529845", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.68061, 0.08614, 0.31496, 0.0705, 0.77001, 0.99513, 0.53747, 0.57677, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [28895, "SRR26821450", "SRX22518175", "SRS19529844", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "10mT fractured 1", "GSM7898624", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing", "10mT fractured 1", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs", "GSM7898624", "GSM7898624: 10mT fractured 1; Danio rerio; RNA Seq", "GSM7898624 r1", "GSM7898624", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "10mT_fractured_1_R2.fq.gz 10mT_fractured_1_R1.fq.gz", "fastq fastq", 1718495100.0, 5728317.0, "GSM7898624 r1", "0:150 1:150", "A:452779669;C:319880075;G:491162181;T:454320323;N:352852", 150, 150, null, null, 452779669, 319880075, 491162181, 454320323, 352852, "SRX22518175", "SRS19529844", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.67153, 0.10745, 0.32942, 0.08781, 0.76775, 0.99427, 0.53417, 0.5895, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [28896, "SRR26821451", "SRX22518174", "SRS19529843", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "0mT fractured 3", "GSM7898623", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing", "0mT fractured 3", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs", "GSM7898623", "GSM7898623: 0mT fractured 3; Danio rerio; RNA Seq", "GSM7898623 r1", "GSM7898623", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "0mT_fractured_3_R1.fq.gz 0mT_fractured_3_R2.fq.gz", "fastq fastq", 1468748700.0, 4895829.0, "GSM7898623 r1", "0:150 1:150", "A:378980971;C:273130967;G:441424422;T:374917129;N:295211", 150, 150, null, null, 378980971, 273130967, 441424422, 374917129, 295211, "SRX22518174", "SRS19529843", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.67867, 0.10573, 0.35963, 0.0899, 0.75982, 0.99508, 0.53209, 0.48863, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [28897, "SRR26821452", "SRX22518173", "SRS19529842", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "0mT fractured 2", "GSM7898622", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing", "0mT fractured 2", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs", "GSM7898622", "GSM7898622: 0mT fractured 2; Danio rerio; RNA Seq", "GSM7898622 r1", "GSM7898622", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "0mT_fractured_2_R1.fq.gz 0mT_fractured_2_R2.fq.gz", "fastq fastq", 2406885600.0, 8022952.0, "GSM7898622 r1", "0:150 1:150", "A:646926387;C:366751040;G:726614721;T:666425874;N:167578", 150, 150, null, null, 646926387, 366751040, 726614721, 666425874, 167578, "SRX22518173", "SRS19529842", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.67096, 0.06177, 0.27169, 0.04875, 0.77492, 0.99805, 0.55512, 0.62711, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [28898, "SRR26821453", "SRX22518172", "SRS19529841", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "0mT fractured 1", "GSM7898621", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing", "0mT fractured 1", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs", "GSM7898621", "GSM7898621: 0mT fractured 1; Danio rerio; RNA Seq", "GSM7898621 r1", "GSM7898621", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "0mT_fractured_1_R1.fq.gz 0mT_fractured_1_R2.fq.gz", "fastq fastq", 2084550000.0, 6948500.0, "GSM7898621 r1", "0:150 1:150", "A:567504433;C:327104215;G:627285267;T:562454734;N:201351", 150, 150, null, null, 567504433, 327104215, 627285267, 562454734, 201351, "SRX22518172", "SRS19529841", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.68491, 0.14639, 0.35327, 0.12371, 0.76459, 0.99584, 0.52889, 0.52678, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [28899, "SRR26821454", "SRX22518171", "SRS19529840", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "Int 3", "GSM7898620", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing", "Int 3", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Intact scales", "GSM7898620", "GSM7898620: Int 3; Danio rerio; RNA Seq", "GSM7898620 r1", "GSM7898620", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "Int_3_R1.fq.gz Int_3_R2.fq.gz", "fastq fastq", 2081211600.0, 6937372.0, "GSM7898620 r1", "0:150 1:150", "A:561341589;C:327618433;G:629445558;T:562620891;N:185129", 150, 150, null, null, 561341589, 327618433, 629445558, 562620891, 185129, "SRX22518171", "SRS19529840", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.68553, 0.11302, 0.32184, 0.0937, 0.7654, 0.99646, 0.53135, 0.50819, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [28900, "SRR26821455", "SRX22518170", "SRS19529839", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "Int 2", "GSM7898619", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing", "Int 2", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Intact scales", "GSM7898619", "GSM7898619: Int 2; Danio rerio; RNA Seq", "GSM7898619 r1", "GSM7898619", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "Int_2_R1.fq.gz Int_2_R2.fq.gz", "fastq fastq", 1639167900.0, 5463893.0, "GSM7898619 r1", "0:150 1:150", "A:445245908;C:275437900;G:483637484;T:434649575;N:197033", 150, 150, null, null, 445245908, 275437900, 483637484, 434649575, 197033, "SRX22518170", "SRS19529839", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.68102, 0.1645, 0.41429, 0.1457, 0.76641, 0.9964, 0.53665, 0.50264, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [28901, "SRR26821456", "SRX22518169", "SRS19529838", "SRP471728", "PRJNA1040136", "Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs", "GSE247669", "Transcriptome Analysis", "The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts  osteoclasts  and bone matrix  providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study  we have performed RNA seq analysis on intact scales  fractured scales not exposed to ELF EMFs  and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.", null, "pubmed:38385024", null, "Int 1", "GSM7898618", null, "source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing", "Int 1", "Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample.", "Whole scales", null, "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "tissue:Whole scales|genotype:Wild type|treatment:Intact scales", "GSM7898618", "GSM7898618: Int 1; Danio rerio; RNA Seq", "GSM7898618 r1", "GSM7898618", "1", "Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT  the index sequence  and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter  and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "Int_1_R1.fq.gz Int_1_R2.fq.gz", "fastq fastq", 2309186700.0, 7697289.0, "GSM7898618 r1", "0:150 1:150", "A:625174483;C:362587163;G:697384210;T:623845956;N:194888", 150, 150, null, null, 625174483, 362587163, 697384210, 623845956, 194888, "SRX22518169", "SRS19529838", "SRA1750892", "Kanazawa University", "Kanazawa University", 2, 0.68814, 0.09858, 0.30026, 0.08284, 0.77315, 0.99768, 0.53387, 0.50406, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [47613, "SRR6760977", "SRX3733411", "SRS2990508", "SRP133266", "PRJNA434353", "Transcriptome assemblies 10 vertebrate species", "PRJNA434353", "Other", "2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human  mouse  cow  tasmanian devil  chicken  duck  zebra finch  xenopus  medaka and zebrafish  4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.", null, null, "4 replicates", null, "Zebrafish", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome assemblies 10 vertebrate species", "zebrafish replicate2", "zebrafish replicate2", "Zebrafish sample replicate 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP133266", null, null, "Sample_imb_butter_2014_04_30_zebrafish_B_R2.fastq.gz 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mouse  cow  tasmanian devil  chicken  duck  zebra finch  xenopus  medaka and zebrafish  4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.", null, null, "4 replicates", null, "Zebrafish", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome assemblies 10 vertebrate species", "zebrafish replicate1", "zebrafish replicate1", "Zebrafish sample replicate 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP133266", null, null, "Sample_imb_butter_2014_04_29_zebrafish_A_R1.fastq.gz Sample_imb_butter_2014_04_29_zebrafish_A_R2.fastq.gz", "fastq fastq", 7117920864.0, 35237232.0, "Sample imb butter 2014 04 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"strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome assemblies 10 vertebrate species", "zebrafish replicate3", "zebrafish replicate3", "Zebrafish sample replicate 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP133266", null, null, "Sample_imb_butter_2014_04_31_zebrafish_C_R1.fastq.gz Sample_imb_butter_2014_04_31_zebrafish_C_R2.fastq.gz", "fastq fastq", 5889796416.0, 29157408.0, "Sample imb butter 2014 04 31 zebrafish C R1.fastq.gz", "0:101 1:101", "A:1629550499;C:1313886355;G:1293890602;T:1636478119;N:15990841", 101, 101, null, null, 1629550499, 1313886355, 1293890602, 1636478119, 15990841, "SRX3733406", "SRS2990508", "SRA660975", "Institute of Molecular 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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.", null, "pubmed:37459514", null, "Zebrafish scale 30mm  replicate 2", "GSM7498272", null, "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 \u2018aggregated\u2019 transcript count for each gene as described by Martik et al.  2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti\u2212minT/maxT\u2212minT 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. 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The libraries were built according to Illumina Standard Protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP445049", null, null, "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, null, null, null, 867694073, 728518022, 750424718, 885367521, 1419566, "SRX20733648", "SRS18024487", "SRA1659604", "Bronner, California Institute of Technology", "Bronner, California Institute of Technology", 1, 0.89607, null, 0.08896, null, 0.72612, null, 0.4695, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:37459514", null, "Zebrafish scale 30mm  replicate 1", "GSM7498271", null, "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 \u2018aggregated\u2019 transcript count for each gene as described by Martik et al.  2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti\u2212minT/maxT\u2212minT 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", null, "RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP445049", null, null, "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, null, null, null, 764903871, 640842328, 660536366, 780092458, 1264377, "SRX20733647", "SRS18024486", "SRA1659604", "Bronner, California Institute of Technology", "Bronner, California Institute of Technology", 1, 0.89576, null, 0.08353, null, 0.73594, null, 0.45703, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-20", "Undetermined", "Undetermined", "Scale", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 27, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", 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