RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

16 rows where devstage_curation_coarse = "Undetermined" and tissue_curation = "Scale"

✎ View and edit SQL

This data as json, CSV (advanced)

technology 3

experiment.library_source 2

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Scale · 16 ✖

experiment.platform 1

experiment.library_strategy 1

devstage_curation_coarse 1

  • Undetermined · 16 ✖

devstage_curation 1

Link 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
28893 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.   pubmed:38385024   10mT fractured 3 GSM7898626   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28894 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.   pubmed:38385024   10mT fractured 2 GSM7898625   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28895 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.   pubmed:38385024   10mT fractured 1 GSM7898624   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28896 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.   pubmed:38385024   0mT fractured 3 GSM7898623   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28897 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.   pubmed:38385024   0mT fractured 2 GSM7898622   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28898 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.   pubmed:38385024   0mT fractured 1 GSM7898621   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28899 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.   pubmed:38385024   Int 3 GSM7898620   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28900 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.   pubmed:38385024   Int 2 GSM7898619   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28901 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.   pubmed:38385024   Int 1 GSM7898618   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     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     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   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
47613 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.     4 replicates   Zebrafish   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                 Transcriptome assemblies 10 vertebrate species zebrafish replicate2 zebrafish replicate2 Zebrafish sample replicate 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_30_zebrafish_B_R2.fastq.gz Sample_imb_butter_2014_04_30_zebrafish_B_R1.fastq.gz fastq fastq 8021078014.0 39708307.0 Sample imb butter 2014 04 30 zebrafish B R2.fastq.gz 0:101 1:101 A:2198831905;C:1810184353;G:1779924959;T:2210094554;N:22042243 101 101     2198831905 1810184353 1779924959 2210094554 22042243 SRX3733411 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.94194 0.93911 0.07724 0.08406 0.75724 0.75558 0.47712 0.49049 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2019-02-15 Undetermined Undetermined Scale Surface Structure
47614 47614 SRR6760978 SRX3733410 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.     4 replicates   Zebrafish   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                 Transcriptome assemblies 10 vertebrate species zebrafish replicate1 zebrafish replicate1 Zebrafish sample replicate 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     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 29 zebrafish A R2.fastq.gz 0:101 1:101 A:1980152632;C:1580333689;G:1558362064;T:1979596193;N:19476286 101 101     1980152632 1580333689 1558362064 1979596193 19476286 SRX3733410 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.9342 0.93044 0.08741 0.09642 0.75674 0.75497 0.49192 0.46492 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2018-02-22 Undetermined Undetermined Scale Surface Structure
47615 47615 SRR6760981 SRX3733407 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.     4 replicates   Zebrafish   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                 Transcriptome assemblies 10 vertebrate species zebrafish replicate4 zebrafish replicate4 Zebrafish sample replicate 4     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_32_zebrafish_D_R1.fastq.gz Sample_imb_butter_2014_04_32_zebrafish_D_R2.fastq.gz fastq fastq 8570683654.0 42429127.0 Sample imb butter 2014 04 32 zebrafish D R1.fastq.gz 0:101 1:101 A:2343151377;C:1943560489;G:1909682494;T:2350658549;N:23630745 101 101     2343151377 1943560489 1909682494 2350658549 23630745 SRX3733407 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.94036 0.94349 0.0838 0.0779 0.75538 0.75737 0.4881 0.48296 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2019-02-15 Undetermined Undetermined Scale Surface Structure
47616 47616 SRR6760982 SRX3733406 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.     4 replicates   Zebrafish   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                 Transcriptome assemblies 10 vertebrate species zebrafish replicate3 zebrafish replicate3 Zebrafish sample replicate 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     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     1629550499 1313886355 1293890602 1636478119 15990841 SRX3733406 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.93285 0.93628 0.09745 0.0871 0.7586 0.7611 0.47374 0.47763 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2018-02-22 Undetermined Undetermined Scale Surface Structure
76470 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 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
76724 76724 SRR25288286 SRX21031899 SRS18304345 SRP449631 PRJNA994919 Diverse Epithelial Lymphocytes in Zebrafish Revealed Using a Novel Scale Biopsy Method GSE237417 Transcriptome Analysis Zebrafish Danio rerio are a compelling model to study lymphocytes because zebrafish and humans have similar adaptive immune systems including their lymphocytes. Antibodies that recognize zebrafish proteins are sparse so many investigators utilize transgenic lymphocyte specific fluorophore labeled lines. Human and zebrafish lymphocyte types are conserved but many aspects of zebrafish lymphocyte biology remain uninvestigated including lymphocytes in peripheral tissues like epidermis. Here we report the first study focused on zebrafish epidermal lymphocytes using scales. Obtaining zebrafish blood via non lethal methods is difficult; scales represent a source to longitudinally sample live fish. We developed a novel biopsy technique collecting scales to analyze epithelial lymphocytes from several fluorescently labeled lines. We imaged scales via confocal microscopy and demonstrated multiple lymphocyte types in scales/epidermis quantifying them flow cytometrically. We profiled gene expression of scale thymic and marrow lymphocytes from the same animals revealing B and T lineage signatures. Single cell qRT PCR and RNA sequencing scRNA seq show not only canonical B and T cells but also novel lymphocyte populations not described previously. To validate longitudinal scale biopsies we serially sampled scales from fish treated with dexamethasone DXM demonstrating epidermal lymphocyte responses. To analyze cells functionally we employed a bead ingestion assay showing thymic marrow and epidermal lymphocytes have phagocytic activity. In summary we establish a novel non lethal technique to obtain zebrafish lymphocytes providing the first quantification expression profiling and functional data DXM responses and phagocytosis from epidermal lymphocytes in the zebrafish model. Overall design: This experimental study aimed to investigate the gene expression profiles of individual lymphocytes from the zebrafish lck:GFP transgenic line by using single cell RNA sequencing scRNA seq analysis. We performed scRNA …   pubmed:39503619   Scale S3 GSM7611261   source name:Scale|tissue:Scale|cell line:NA|cell type:Lymphocytes|genotype:lck:GFP|geo loc name:missing|collection date:missing Scale S3 post conversion to fastq files reads for each sample were processed and aggregated using the 10x Genomics Cell Ranger v.6.0.0 pipeline no normalization default settings and processed in the Seurat R package v.4.3.0. We obtained transcriptomes for 6 359 cells post Cell Ranger processing. SoupX v.1.6.2 was used to model and remove ambient RNA contamination per sample and scDblFinder v.1.12.0 was used to detect potential multiplets default settings per individual tissue type. Additional QC filtering was performed to remove potential dead or dying cells along with cells exhibiting abnormal read/gene counts and high levels of mitochondrial transcripts resulting in 1 890 usable cells for our analysis. Using fastMNN cells were normalized and integrated and then clustered within Seurat Leiden algorithm. Clustering resolution was optimized using the clustree package v.0.5.0. Cluster boundaries were manually examined and fine tuned to optimize biological interpretation. Collective diagnostic gene signatures corresponding to published gene lists and our own sc qRT PCR results were explored using Seurat and UCell v.2.2.0. Preferential gene markers were determined for each distinct population using the FindAllMarkers function within Seurat to aid in cell type assignment p.adj ≤ 0.05 min.pct = 0.25. Assembly: GRCz11 Supplementary files format and content: Tab delimited value files and matrices. Scale   For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymus kidney marrow and scale samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating tissues using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. Following creation of single cell emulsions uniquely identifiable 1st strand template single cell cDNA libraries were generated from each cell by emulsion PCR. 2nd strand cDNA was generated and ligated to compatible Illumina adapters. Libraries were loaded onto single NovaSeq 6000 lanes and sequenced using read lengths of 28 bp for the first read 120 bp for the second read and 8 base index reads.   tissue:Scale|cell line:NA|cell type:Lymphocytes|genotype:lck:GFP GSM7611261 GSM7611261: Scale S3; Danio rerio; RNA Seq GSM7611261 r1 GSM7611261 1 For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymus kidney marrow and scale samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating tissues using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. Following creation of single cell emulsions uniquely identifiable 1st strand template single cell cDNA libraries were generated from each cell by emulsion PCR. 2nd strand cDNA was generated and ligated to compatible Illumina adapters. Libraries were loaded onto single NovaSeq 6000 lanes and sequenced using read lengths of 28 bp for the first read 120 bp for the second read and 8 base index reads.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP449631   loader:fastq load.py 3_Mo_1ck_Scale_S3_L001_I1_001.fastq.gz 3_Mo_1ck_Scale_S3_L001_R1_001.fastq.gz 3_Mo_1ck_Scale_S3_L001_R2_001.fastq.gz fastq fastq fastq 13856601096.0 88824366.0 GSM7611261 r1 0:8 1:28 2:120 A:3100061291;C:2322303742;G:2574066837;T:2662358757;N:133293 8 28 120   3100061291 2322303742 2574066837 2662358757 133293 SRX21031899 SRS18304345 SRA1673435 Pediatrics, University of Oklahoma Health Sciences Center Pediatrics, University of Oklahoma Health Sciences Center 1 0.91797   0.2174   0.84145   0.602   120   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-07-14 Undetermined Undetermined Scale Surface Structure

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;