metadata: run_metadata: 18 rows where experiment.library_layout = "PAIRED", tissue_curation = "Scale" and tissue_curation

18 rows where experiment.library_layout = "PAIRED", tissue_curation = "Scale" and tissue_curation_coarse = "Surface Structure"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	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
71632	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…	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	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…	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	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…	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	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…	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
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

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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");;