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,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,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,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,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,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,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,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,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,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
71632,SRR21855290,SRX17843605,SRS15365430,SRP401856,PRJNA889065,A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish,GSE215189,Transcriptome Analysis,T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.,,pubmed:37155881,,Infected  scRNAseq,GSM6625507,,tissue:Descaled cells|cell type:Descaled cells|treatment:infected,Infected  scRNAseq,Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files,Descaled cells,,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2  10x Genomics.,,cell type:Descaled cells|treatment:infected,GSM6625507,GSM6625507: Infected  scRNAseq; Danio rerio; RNA Seq,GSM6625507 r1,GSM6625507,1,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP401856,,loader:fastq load.py,Infected_S2_L001_R1_001.fastq.gz Infected_S2_L001_R2_001.fastq.gz,fastq fastq,27971148231.0,239069643.0,GSM6625507 r1,0:28 1:89,A:8061885724;C:6040148313;G:6562354866;T:7306186742;N:572586,28,89,,,8061885724,6040148313,6562354866,7306186742,572586,SRX17843605,SRS15365430,SRA1517576,"Ting Wang, Genetics, Washington University St Louis","Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health",2,0.00829,0.90109,0.0031,0.16974,0.98742,0.79249,0.29098,0.56795,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2022-10-10,Adult,Adult,Scale,Surface Structure
71633,SRR21855291,SRX17843605,SRS15365430,SRP401856,PRJNA889065,A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish,GSE215189,Transcriptome Analysis,T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.,,pubmed:37155881,,Infected  scRNAseq,GSM6625507,,tissue:Descaled cells|cell type:Descaled cells|treatment:infected,Infected  scRNAseq,Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files,Descaled cells,,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2  10x Genomics.,,cell type:Descaled cells|treatment:infected,GSM6625507,GSM6625507: Infected  scRNAseq; Danio rerio; RNA Seq,GSM6625507 r1,GSM6625507,1,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP401856,,loader:fastq load.py,Infected_S2_L002_R1_001.fastq.gz Infected_S2_L002_R2_001.fastq.gz,fastq fastq,28948392252.0,247422156.0,GSM6625507 r2,0:28 1:89,A:8329225374;C:6258698724;G:6802339342;T:7557690208;N:438604,28,89,,,8329225374,6258698724,6802339342,7557690208,438604,SRX17843605,SRS15365430,SRA1517576,"Ting Wang, Genetics, Washington University St Louis","Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health",2,0.00815,0.89934,0.00296,0.16878,0.98717,0.79032,0.32081,0.56999,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2022-10-10,Adult,Adult,Scale,Surface Structure
71634,SRR21855292,SRX17843604,SRS15365429,SRP401856,PRJNA889065,A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish,GSE215189,Transcriptome Analysis,T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.,,pubmed:37155881,,Control  scRNAseq,GSM6625506,,tissue:Descaled cells|cell type:Descaled cells|treatment:control,Control  scRNAseq,Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files,Descaled cells,,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2  10x Genomics.,,cell type:Descaled cells|treatment:control,GSM6625506,GSM6625506: Control  scRNAseq; Danio rerio; RNA Seq,GSM6625506 r1,GSM6625506,1,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP401856,,loader:fastq load.py,Control_S1_L001_R1_001.fastq.gz Control_S1_L001_R2_001.fastq.gz,fastq fastq,22227506496.0,189978688.0,GSM6625506 r1,0:28 1:89,A:6692049340;C:4739918301;G:5329051962;T:5466033150;N:453743,28,89,,,6692049340,4739918301,5329051962,5466033150,453743,SRX17843604,SRS15365429,SRA1517576,"Ting Wang, Genetics, Washington University St Louis","Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health",2,0.01277,0.88905,0.00634,0.17657,0.98879,0.78119,0.33278,0.56433,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2022-10-10,Adult,Adult,Scale,Surface Structure
71635,SRR21855293,SRX17843604,SRS15365429,SRP401856,PRJNA889065,A Tessellated Lymphoid Network Provides Whole Body Antigen Surveillance in Zebrafish,GSE215189,Transcriptome Analysis,T cells survey the host for cognate antigen in mammals by trafficking to and searching within lymph nodes distributed throughout the body. Non mammalian jawed vertebrates lack lymph nodes but still maintain highly diverse repertoires of T cells. How these T cells find antigen in hosts devoid of lymph nodes remains wholly unclear. In this study  we exploit the in vivo imaging amenability of the zebrafish to investigate T cell organization  trafficking  and antigen surveillance in an animal completely lacking lymph nodes. We find that T cells organize into a previously undescribed whole body scale associated pattern that we have named the tessellated lymphoid network TLN. We find that the TLN harbors significantly more T cells than the gills  gut  kidney  and spleen  as well as populations of antigen presenting cells  suggesting a central role in adaptive immune responses in fish. Within the TLN  T cells perform a highly directional ballistic streaming mode of motility  allowing them to traffic through the host in a coordinated ventral to dorsal loop. Local infection results in a dramatic shift in T cell motility  from rapid streaming to a slower random walk in regions proximal to the infection. Here  T cells sequentially interact with and ultimately form stable contacts with antigen presenting cells. Finally  T cells within the TLN of infected fish show transcriptional changes consistent with TCR signaling and subsequent T cell activation. The TLN thus provides a mechanism for T cells to both traffic through the host and  in the context of an infection  effectively scan for and detect antigen  mirroring the function of lymph nodes in mammals. Overall design: Adult zebrafish either without xxx or infected by L. monocytogenes through puncture wounding were euthanized and descaled to collect associated cells at 4 days post infection. Libraries were constructed from these cells using the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and sequenced using NovaSeq6000 Illumina with read lengths of 29 bp + 90 bp Read1 + Read2.,,pubmed:37155881,,Control  scRNAseq,GSM6625506,,tissue:Descaled cells|cell type:Descaled cells|treatment:control,Control  scRNAseq,Raw FASTQ files were processed by cellranger 6.1.2 10x Genomics for demultiplexing  barcoded processing  and gene counting. Assembly: zv11 Supplementary files format and content: Tab separated values files and matrix files,Descaled cells,,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter’s instructions Chromium Single Cell Gene Expression Solution 3’ v2  10x Genomics.,,cell type:Descaled cells|treatment:control,GSM6625506,GSM6625506: Control  scRNAseq; Danio rerio; RNA Seq,GSM6625506 r1,GSM6625506,1,Euthanized adult zebrafish were briefly dunked in room temperature phosphate buffered saline PBS  Gibco 14190 144 and then placed in a 60mm Petri Dish Fisher FB0875713A containing 8 milliliters of room temperature PBS. One gloved hand was used to hold the fish in place by firmly grasping the head  and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife Fine Science Tools 10056 12 to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal  dorsal  and anal fins typically had to be individually removed by plucking with thin tip tweezers Dumont. PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette Fisher 13 711 7M to promote cells entering the suspension  and the buffer was then passed through a 40 micron filter. This cell suspension was then mixed 1:1 with cell isolation media L 15  penicillin streptomycin  and 2% FBS in a 15 mL falcon tube  washed  resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells  and washed once more with cell isolation media. Library was performed according to the manufacter's instructions Chromium Single Cell Gene Expression Solution three prime v2  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP401856,,loader:fastq load.py,Control_S1_L002_R1_001.fastq.gz Control_S1_L002_R2_001.fastq.gz,fastq fastq,22948305003.0,196139359.0,GSM6625506 r2,0:28 1:89,A:6891536928;C:4902194962;G:5508766043;T:5645479908;N:327162,28,89,,,6891536928,4902194962,5508766043,5645479908,327162,SRX17843604,SRS15365429,SRA1517576,"Ting Wang, Genetics, Washington University St Louis","Anna Huttenlocher, Pediatrics, University of Wisconsin School of Medicine and Public Health",2,0.01284,0.88937,0.00623,0.17647,0.98926,0.78315,0.32038,0.56842,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2022-10-10,Adult,Adult,Scale,Surface Structure
76470,SRR24976460,SRX20733648,SRS18024487,SRP445049,PRJNA985650,Ancient vertebrate dermal armor evolved from trunk neural crest,GSE235280,Other,Bone is an evolutionary novelty of vertebrates  likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor  we have performed in vivo lineage tracing in the sterlet sturgeon  a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally  histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone  dentin and hypermineralized covering tissues  in various combinations  that resemble those of the first armored vertebrates. Taken together  our results support a primitive skeletogenic role for the neural crest along the entire body axis  that was later progressively restricted to the cranial region during vertebrate evolution. Thus  the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor  we performed bulk RNA sequencing of sterlet sturgeon scutes  scales of the Senegal bichir  and zebrafish scales.,,pubmed:37459514,,Zebrafish scale 30mm  replicate 2,GSM7498272,,source name:cells of elasmoid scale|tissue:cells of elasmoid scale|genotype:WT|measure:30 mm|geo loc name:missing|collection date:missing,Zebrafish scale 30mm  replicate 2,In brief  every sterlet/bichir protein sequence was queried locally against the zebrafish proteome  following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach  proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences  while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference  we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al.  2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample,cells of elasmoid scale,,RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.,,tissue:cells of elasmoid scale|genotype:WT|measure:30 mm,GSM7498272,GSM7498272: Zebrafish scale 30mm  replicate 2; Danio rerio; RNA Seq,GSM7498272 r1,GSM7498272,1,RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP445049,,,DR_scale_2.fastq.gz,fastq,3233423900.0,64668478.0,GSM7498272 r1,0:50,A:867694073;C:728518022;G:750424718;T:885367521;N:1419566,50,,,,867694073,728518022,750424718,885367521,1419566,SRX20733648,SRS18024487,SRA1659604,"Bronner, California Institute of Technology","Bronner, California Institute of Technology",1,0.89607,,0.08896,,0.72612,,0.4695,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-06-20,Undetermined,Undetermined,Scale,Surface Structure
76471,SRR24976461,SRX20733647,SRS18024486,SRP445049,PRJNA985650,Ancient vertebrate dermal armor evolved from trunk neural crest,GSE235280,Other,Bone is an evolutionary novelty of vertebrates  likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor  we have performed in vivo lineage tracing in the sterlet sturgeon  a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally  histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone  dentin and hypermineralized covering tissues  in various combinations  that resemble those of the first armored vertebrates. Taken together  our results support a primitive skeletogenic role for the neural crest along the entire body axis  that was later progressively restricted to the cranial region during vertebrate evolution. Thus  the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor  we performed bulk RNA sequencing of sterlet sturgeon scutes  scales of the Senegal bichir  and zebrafish scales.,,pubmed:37459514,,Zebrafish scale 30mm  replicate 1,GSM7498271,,source name:cells of elasmoid scale|tissue:cells of elasmoid scale|genotype:WT|measure:30 mm|geo loc name:missing|collection date:missing,Zebrafish scale 30mm  replicate 1,In brief  every sterlet/bichir protein sequence was queried locally against the zebrafish proteome  following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach  proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences  while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference  we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al.  2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample,cells of elasmoid scale,,RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.,,tissue:cells of elasmoid scale|genotype:WT|measure:30 mm,GSM7498271,GSM7498271: Zebrafish scale 30mm  replicate 1; Danio rerio; RNA Seq,GSM7498271 r1,GSM7498271,1,RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP445049,,,DR_scale_1.fastq.gz,fastq,2847639400.0,56952788.0,GSM7498271 r1,0:50,A:764903871;C:640842328;G:660536366;T:780092458;N:1264377,50,,,,764903871,640842328,660536366,780092458,1264377,SRX20733647,SRS18024486,SRA1659604,"Bronner, California Institute of Technology","Bronner, California Institute of Technology",1,0.89576,,0.08353,,0.73594,,0.45703,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2023-06-20,Undetermined,Undetermined,Scale,Surface Structure
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 seq on GFPhi thymocytes and GFPlo scale/marrow cells from lck:GFP fish which mark different lymphocyte populations. scRNA seq data reveal diverse thymic  scale  and marrow lymphocyte populations for subsequent transcriptomic analysis and isolation of specific cell types.,,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