metadata: run_metadata: 11 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC" and tissue

11 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC" 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
76470	76470	SRR24976460	SRX20733648	SRS18024487	SRP445049	PRJNA985650	Ancient vertebrate dermal armor evolved from trunk neural crest	GSE235280	Other	Bone is an evolutionary novelty of vertebrates likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor we have performed in vivo lineage tracing in the sterlet sturgeon a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone dentin and hypermineralized covering tissues in various combinations that resemble those of the first armored vertebrates. Taken together our results support a primitive skeletogenic role for the neural crest along the entire body axis that was later progressively restricted to the cranial region during vertebrate evolution. Thus the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor we performed bulk RNA sequencing of sterlet sturgeon scutes scales of the Senegal bichir and zebrafish scales.	pubmed:37459514	Zebrafish scale 30mm replicate 2	GSM7498272	source name:cells of elasmoid scale\|tissue:cells of elasmoid scale\|genotype:WT\|measure:30 mm\|geo loc name:missing\|collection date:missing	Zebrafish scale 30mm replicate 2	In brief every sterlet/bichir protein sequence was queried locally against the zebrafish proteome following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al. 2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample	cells of elasmoid scale	RNAqueous kit Ambion prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.	tissue:cells of elasmoid scale\|genotype:WT\|measure:30 mm	GSM7498272	GSM7498272: Zebrafish scale 30mm replicate 2; Danio rerio; RNA Seq	GSM7498272 r1	GSM7498272	1	RNAqueous kit Ambion prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP445049	DR_scale_2.fastq.gz	fastq	3233423900.0	64668478.0	GSM7498272 r1	0:50	A:867694073;C:728518022;G:750424718;T:885367521;N:1419566	50		867694073	728518022	750424718	885367521	1419566	SRX20733648	SRS18024487	SRA1659604	Bronner, California Institute of Technology	Bronner, California Institute of Technology	1	0.89607		0.08896		0.72612		0.4695		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2023-06-20	Undetermined	Undetermined	Scale	Surface Structure
76471	76471	SRR24976461	SRX20733647	SRS18024486	SRP445049	PRJNA985650	Ancient vertebrate dermal armor evolved from trunk neural crest	GSE235280	Other	Bone is an evolutionary novelty of vertebrates likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor we have performed in vivo lineage tracing in the sterlet sturgeon a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone dentin and hypermineralized covering tissues in various combinations that resemble those of the first armored vertebrates. Taken together our results support a primitive skeletogenic role for the neural crest along the entire body axis that was later progressively restricted to the cranial region during vertebrate evolution. Thus the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor we performed bulk RNA sequencing of sterlet sturgeon scutes scales of the Senegal bichir and zebrafish scales.	pubmed:37459514	Zebrafish scale 30mm replicate 1	GSM7498271	source name:cells of elasmoid scale\|tissue:cells of elasmoid scale\|genotype:WT\|measure:30 mm\|geo loc name:missing\|collection date:missing	Zebrafish scale 30mm replicate 1	In brief every sterlet/bichir protein sequence was queried locally against the zebrafish proteome following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al. 2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample	cells of elasmoid scale	RNAqueous kit Ambion prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.	tissue:cells of elasmoid scale\|genotype:WT\|measure:30 mm	GSM7498271	GSM7498271: Zebrafish scale 30mm replicate 1; Danio rerio; RNA Seq	GSM7498271 r1	GSM7498271	1	RNAqueous kit Ambion prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP445049	DR_scale_1.fastq.gz	fastq	2847639400.0	56952788.0	GSM7498271 r1	0:50	A:764903871;C:640842328;G:660536366;T:780092458;N:1264377	50		764903871	640842328	660536366	780092458	1264377	SRX20733647	SRS18024486	SRA1659604	Bronner, California Institute of Technology	Bronner, California Institute of Technology	1	0.89576		0.08353		0.73594		0.45703		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2023-06-20	Undetermined	Undetermined	Scale	Surface Structure

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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");;