{"database": "metadata", "table": "run_metadata", "rows": [[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.", null, "pubmed:38385024", null, "0mT fractured 2", "GSM7898622", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP471728", null, null, "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, null, null, 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", null, "Japan", "2023-11-14", "Undetermined", "Undetermined", "Scale", "Surface Structure"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["28897"], "units": {}, "query_ms": 9.666861000368954}