metadata: run_metadata: 9 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue

9 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation = "Scale"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	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.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.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

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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");;