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 201,DRR162540,DRX153159,DRS083220,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate5,SAMD00152488,,sample name:m02 5|age:2 month|biological replicate:5|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152488,DRX153159,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152488,,,,1063436200.0,5317181.0,DRR162540,0:100 1:100,A:275438061;C:255805442;G:257091950;T:273487067;N:1613680,100,100,,,275438061,255805442,257091950,273487067,1613680,DRX153159,DRS083220,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96295,0.92896,0.04409,0.0427,0.75355,0.76499,0.49339,0.50418,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System 202,DRR162539,DRX153158,DRS083219,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate4,SAMD00152487,,sample name:m02 4|age:2 month|biological replicate:4|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152487,DRX153158,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152487,,,,1233640200.0,6168201.0,DRR162539,0:100 1:100,A:318959646;C:297211942;G:300002324;T:315647570;N:1818718,100,100,,,318959646,297211942,300002324,315647570,1818718,DRX153158,DRS083219,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96511,0.92512,0.04175,0.04058,0.77607,0.78835,0.48689,0.50535,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System 203,DRR162538,DRX153157,DRS083218,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate3,SAMD00152486,,sample name:m02 3|age:2 month|biological replicate:3|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152486,DRX153157,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152486,,,,675957200.0,3379786.0,DRR162538,0:100 1:100,A:173033870;C:164578076;G:165481544;T:171780353;N:1083357,100,100,,,173033870,164578076,165481544,171780353,1083357,DRX153157,DRS083218,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.97251,0.94405,0.03347,0.03256,0.82432,0.83159,0.55228,0.47905,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System 204,DRR162537,DRX153156,DRS083217,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate2,SAMD00152485,,sample name:m02 2|age:2 month|biological replicate:2|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152485,DRX153156,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152485,,,,1260768000.0,6303840.0,DRR162537,0:100 1:100,A:319433176;C:310903964;G:312279388;T:316219239;N:1932233,100,100,,,319433176,310903964,312279388,316219239,1932233,DRX153156,DRS083217,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96774,0.93275,0.04099,0.04003,0.76919,0.79626,0.51687,0.50638,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System 205,DRR162536,DRX153155,DRS083216,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate1,SAMD00152484,,sample name:m02 1|age:2 month|biological replicate:1|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152484,DRX153155,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152484,,,,1318898400.0,6594492.0,DRR162536,0:100 1:100,A:337402722;C:321381897;G:323422706;T:334658718;N:2032357,100,100,,,337402722,321381897,323422706,334658718,2032357,DRX153155,DRS083216,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9692,0.93768,0.02944,0.02852,0.79431,0.80359,0.50636,0.51065,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System 64385,SRR14679147,SRX11017528,SRS9089834,SRP321802,PRJNA733247,Danio rerio breed:Danio Raw sequence reads,PRJNA733247,Whole Genome Sequencing,zebrafish muscle tissue for scRNA seq and bulk RNA seq,,,,Model organism or animal sample from Danio rerio,zebrafish,,breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,bulk RNA seq,runx2b+/+ 2 bulk RNA seq,runx2b+/+ 2 bulk RNA seq,tail muscle with intermuscular bone,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP321802,,,WT_2_60dpf.R1.fq.gz WT_2_60dpf.R2.fq.gz,fastq fastq,7007750400.0,23359168.0,WT 2 60dpf.R1.fq.gz,0:150 1:150,A:1714498514;C:1702913716;G:1897215939;T:1693105532;N:16699,150,150,,,1714498514,1702913716,1897215939,1693105532,16699,SRX11017528,SRS9089834,SRA1238123,Huazhong Agricultural university|Huazhong Agricultural university,Huazhong Agricultural university,2,0.93184,0.92606,0.01222,0.01169,0.84762,0.85033,0.67174,0.64259,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2021-05-28,Juvenile,Juvenile,Muscle,Muscular System 64386,SRR14679148,SRX11017527,SRS9089834,SRP321802,PRJNA733247,Danio rerio breed:Danio Raw sequence reads,PRJNA733247,Whole Genome Sequencing,zebrafish muscle tissue for scRNA seq and bulk RNA seq,,,,Model organism or animal sample from Danio rerio,zebrafish,,breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,bulk RNA seq,runx2b+/+ 1 bulk RNA seq,runx2b+/+ 1 bulk RNA seq,tail muscle with intermuscular bone,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP321802,,,WT_1_60dpf.R1.fq.gz WT_1_60dpf.R2.fq.gz,fastq fastq,6785203800.0,22617346.0,WT 1 60dpf.R1.fq.gz,0:150 1:150,A:1660992152;C:1637869425;G:1843210897;T:1643114944;N:16382,150,150,,,1660992152,1637869425,1843210897,1643114944,16382,SRX11017527,SRS9089834,SRA1238123,Huazhong Agricultural university|Huazhong Agricultural university,Huazhong Agricultural university,2,0.92764,0.92197,0.00968,0.00947,0.84323,0.84577,0.65455,0.6592,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2021-05-28,Juvenile,Juvenile,Muscle,Muscular System 64387,SRR14679149,SRX11017526,SRS9089834,SRP321802,PRJNA733247,Danio rerio breed:Danio Raw sequence reads,PRJNA733247,Whole Genome Sequencing,zebrafish muscle tissue for scRNA seq and bulk RNA seq,,,,Model organism or animal sample from Danio rerio,zebrafish,,breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq,runx2b / scRNA seq,runx2b / scRNA seq,tail muscle without xxx bone,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP321802,,,MU_S2_L003_R1_001.fastq.gz MU_S2_L003_R2_001.fastq.gz,fastq fastq,112565768100.0,375219227.0,MU S2 L003 R1 001.fastq.gz,0:150 1:150,A:34329910863;C:17430450121;G:18090145246;T:42713500460;N:1761410,150,150,,,34329910863,17430450121,18090145246,42713500460,1761410,SRX11017526,SRS9089834,SRA1238123,Huazhong Agricultural university|Huazhong Agricultural university,Huazhong Agricultural university,2,0.34692,0.92476,0.05138,0.09375,0.98543,0.82371,0.68433,0.7376,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,bulk,bulk,,China,2021-05-29,Juvenile,Juvenile,Muscle,Muscular System 64388,SRR14679150,SRX11017525,SRS9089834,SRP321802,PRJNA733247,Danio rerio breed:Danio Raw sequence reads,PRJNA733247,Whole Genome Sequencing,zebrafish muscle tissue for scRNA seq and bulk RNA seq,,,,Model organism or animal sample from Danio rerio,zebrafish,,breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq,runx2b+/+ scRNA seq,runx2b+/+ scRNA seq,tail muscle with intermuscular bone,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP321802,,,WT_S1_L003_R1_001.fastq.gz WT_S1_L003_R2_001.fastq.gz,fastq fastq,99838157100.0,332793857.0,WT S1 L003 R1 001.fastq.gz,0:150 1:150,A:30283010374;C:15529232903;G:16181518775;T:37842782328;N:1612720,150,150,,,30283010374,15529232903,16181518775,37842782328,1612720,SRX11017525,SRS9089834,SRA1238123,Huazhong Agricultural university|Huazhong Agricultural university,Huazhong Agricultural university,2,0.34302,0.92611,0.04637,0.09453,0.98701,0.83658,0.71917,0.76074,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,bulk,bulk,,China,2021-05-29,Juvenile,Juvenile,Muscle,Muscular System 64389,SRR14679151,SRX11017524,SRS9089834,SRP321802,PRJNA733247,Danio rerio breed:Danio Raw sequence reads,PRJNA733247,Whole Genome Sequencing,zebrafish muscle tissue for scRNA seq and bulk RNA seq,,,,Model organism or animal sample from Danio rerio,zebrafish,,breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,bulk RNA seq,runx2b / 3 bulk RNA seq,runx2b / 3 bulk RNA seq,tail muscle without xxx bone,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP321802,,,MUT_3_60dpf.R1.fq.gz MUT_3_60dpf.R2.fq.gz,fastq fastq,7358370600.0,24527902.0,MUT 3 60dpf.R1.fq.gz,0:150 1:150,A:1781646726;C:1790446433;G:2025455441;T:1760804227;N:17773,150,150,,,1781646726,1790446433,2025455441,1760804227,17773,SRX11017524,SRS9089834,SRA1238123,Huazhong Agricultural university|Huazhong Agricultural university,Huazhong Agricultural university,2,0.92552,0.9218,0.01223,0.01223,0.86222,0.86348,0.68246,0.64029,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2021-05-28,Juvenile,Juvenile,Muscle,Muscular System 64390,SRR14679152,SRX11017523,SRS9089834,SRP321802,PRJNA733247,Danio rerio breed:Danio Raw sequence reads,PRJNA733247,Whole Genome Sequencing,zebrafish muscle tissue for scRNA seq and bulk RNA seq,,,,Model organism or animal sample from Danio rerio,zebrafish,,breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,bulk RNA seq,runx2b / 2 bulk RNA seq,runx2b / 2 bulk RNA seq,tail muscle without xxx bone,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP321802,,,MUT_2_60dpf.R1.fq.gz MUT_2_60dpf.R2.fq.gz,fastq fastq,5983046100.0,19943487.0,MUT 2 60dpf.R1.fq.gz,0:150 1:150,A:1456794159;C:1460953692;G:1613536834;T:1451747111;N:14304,150,150,,,1456794159,1460953692,1613536834,1451747111,14304,SRX11017523,SRS9089834,SRA1238123,Huazhong Agricultural university|Huazhong Agricultural university,Huazhong Agricultural university,2,0.93491,0.9294,0.01148,0.01117,0.85474,0.85667,0.69448,0.63383,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2021-05-28,Juvenile,Juvenile,Muscle,Muscular System 64391,SRR14679153,SRX11017522,SRS9089834,SRP321802,PRJNA733247,Danio rerio breed:Danio Raw sequence reads,PRJNA733247,Whole Genome Sequencing,zebrafish muscle tissue for scRNA seq and bulk RNA seq,,,,Model organism or animal sample from Danio rerio,zebrafish,,breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,bulk RNA seq,runx2b / 1 bulk RNA seq,runx2b / 1 bulk RNA seq,tail muscle without xxx bone,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP321802,,,MUT_1_60dpf.R1.fq.gz MUT_1_60dpf.R2.fq.gz,fastq fastq,6876053100.0,22920177.0,MUT 1 60dpf.R1.fq.gz,0:150 1:150,A:1683687632;C:1665466650;G:1862910858;T:1663971371;N:16589,150,150,,,1683687632,1665466650,1862910858,1663971371,16589,SRX11017522,SRS9089834,SRA1238123,Huazhong Agricultural university|Huazhong Agricultural university,Huazhong Agricultural university,2,0.93272,0.92802,0.01179,0.01133,0.84861,0.84993,0.62206,0.67726,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2021-05-28,Juvenile,Juvenile,Muscle,Muscular System 64392,SRR14679154,SRX11017521,SRS9089834,SRP321802,PRJNA733247,Danio rerio breed:Danio Raw sequence reads,PRJNA733247,Whole Genome Sequencing,zebrafish muscle tissue for scRNA seq and bulk RNA seq,,,,Model organism or animal sample from Danio rerio,zebrafish,,breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,bulk RNA seq,runx2b+/+ 3 bulk RNA seq,runx2b+/+ 3 bulk RNA seq,tail muscle with intermuscular bone,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP321802,,,WT_3_60dpf.R1.fq.gz WT_3_60dpf.R2.fq.gz,fastq fastq,6834033900.0,22780113.0,WT 3 60dpf.R1.fq.gz,0:150 1:150,A:1665713519;C:1660512523;G:1864685424;T:1643106338;N:16096,150,150,,,1665713519,1660512523,1864685424,1643106338,16096,SRX11017521,SRS9089834,SRA1238123,Huazhong Agricultural university|Huazhong Agricultural university,Huazhong Agricultural university,2,0.92968,0.92349,0.01013,0.01013,0.85811,0.85999,0.62541,0.6776,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2021-05-28,Juvenile,Juvenile,Muscle,Muscular System 66710,SRR16378894,SRX12656337,SRS10609555,SRP341786,PRJNA772011,Spatial transcriptome of zebrafish trunk section,PRJNA772011,Other,Spatial transcriptome sequencing data from sections of adult and larvae zebrafish trunk. Aiming to delineate the distribution of fast and slow muscle fibers in zebrafish by transcriptomic patterns and the regulation of muscle growth.,,,,,zebrafish larvae,,strain:Riken wide type|age:1 month|sex:not applicable|tissue:muscle|birth location:Tokyo Japan|collection date:2020 08 20|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae muscle,zebrafish larva,zebrafish larva,Visium spatial transcriptomics,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP341786,,,zebra_young_S1_L004_R1_001.fastq zebra_young_S1_L004_R2_001.fastq,fastq fastq,2755287020.0,23349890.0,zebra young S1 L004 R1 001.fastq,0:28 1:90,A:775062912;C:621131964;G:654720744;T:704362634;N:8766,28,90,,,775062912,621131964,654720744,704362634,8766,SRX12656337,SRS10609555,SRA1312274,The University of Tokyo|Graduate School of Agriculture and Life Science,The University of Tokyo,2,0.00167,0.91629,0.0005,0.02744,0.99707,0.85989,0.57777,0.51307,28,90,T,B,sc-like readlen,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Japan,2021-10-17,Juvenile,Juvenile,Muscle,Muscular System 66846,SRR16681977,SRX12882565,SRS10825217,SRP344071,PRJNA776888,Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts,GSE186957,Transcriptome Analysis,Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish,,pubmed:39741296,,runx2b / scRNA seq,GSM5664293,,source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ,runx2b / scRNA seq,Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample,muscle and IB,,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,,strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ,GSM5664293,GSM5664293: runx2b / scRNA seq; Danio rerio; RNA Seq,GSM5664293,,1,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,GEO Accession:GSM5664293,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP344071,,loader:fastq load.py,MU_S2_L003_R2_001.fastq MU_S2_L003_R1_001.fastq,fastq fastq,112565768100.0,375219227.0,GSM5664293 r1,0:150 1:150,A:34329910863;C:17430450121;G:18090145246;T:42713500460;N:1761410,150,150,,,34329910863,17430450121,18090145246,42713500460,1761410,SRX12882565,SRS10825217,SRA1320685,GEO,huazhong agricultural university,2,0.34718,0.92478,0.05085,0.09377,0.98545,0.82375,0.7209,0.73759,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_droplet,10x,,China,2021-11-01,Juvenile,Juvenile,Muscle,Muscular System 66847,SRR16681976,SRX12882564,SRS10825216,SRP344071,PRJNA776888,Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts,GSE186957,Transcriptome Analysis,Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish,,pubmed:39741296,,runx2b+/+ scRNA seq,GSM5664292,,source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type,runx2b+/+ scRNA seq,Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample,muscle and IB,,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,,strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type,GSM5664292,GSM5664292: runx2b+/+ scRNA seq; Danio rerio; RNA Seq,GSM5664292,,1,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,GEO Accession:GSM5664292,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP344071,,loader:fastq load.py|options: doNotUseSharq,WT_S1_L003_R1_001.fastq WT_S1_L003_R2_001.fastq,fastq fastq,99838157100.0,332793857.0,GSM5664292 r1,0:150 1:150,A:30283010374;C:15529232903;G:16181518775;T:37842782328;N:1612720,150,150,,,30283010374,15529232903,16181518775,37842782328,1612720,SRX12882564,SRS10825216,SRA1320685,GEO,huazhong agricultural university,2,0.34316,0.92608,0.04623,0.09467,0.98701,0.83644,0.72084,0.76059,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_droplet,10x,,China,2021-11-01,Juvenile,Juvenile,Muscle,Muscular System 66848,SRR16681984,SRX12882563,SRS10825218,SRP344071,PRJNA776888,Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts,GSE186957,Transcriptome Analysis,Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish,,pubmed:39741296,,runx2b / bulk RNA seq rep3,GSM5664299,,source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ,runx2b / bulk RNA seq rep3,Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample,muscle and IB,,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,,strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ,GSM5664299,GSM5664299: runx2b / bulk RNA seq rep3; Danio rerio; RNA Seq,GSM5664299,,1,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,GEO Accession:GSM5664299,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP344071,,loader:fastq load.py,MUT_3_60dpf.R1.fq MUT_3_60dpf.R2.fq,fastq fastq,7358370600.0,24527902.0,GSM5664299 r1,0:150 1:150,A:1781646726;C:1790446433;G:2025455441;T:1760804227;N:17773,150,150,,,1781646726,1790446433,2025455441,1760804227,17773,SRX12882563,SRS10825218,SRA1320685,GEO,huazhong agricultural university,2,0.92553,0.92182,0.01196,0.01201,0.86239,0.86348,0.70266,0.63893,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_droplet,10x,,China,2021-11-01,Juvenile,Juvenile,Muscle,Muscular System 66849,SRR16681983,SRX12882562,SRS10825219,SRP344071,PRJNA776888,Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts,GSE186957,Transcriptome Analysis,Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish,,pubmed:39741296,,runx2b / bulk RNA seq rep2,GSM5664298,,source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ,runx2b / bulk RNA seq rep2,Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample,muscle and IB,,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,,strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ,GSM5664298,GSM5664298: runx2b / bulk RNA seq rep2; Danio rerio; RNA Seq,GSM5664298,,1,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,GEO Accession:GSM5664298,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP344071,,loader:fastq load.py,MUT_2_60dpf.R2.fq MUT_2_60dpf.R1.fq,fastq fastq,5983046100.0,19943487.0,GSM5664298 r1,0:150 1:150,A:1456794159;C:1460953692;G:1613536834;T:1451747111;N:14304,150,150,,,1456794159,1460953692,1613536834,1451747111,14304,SRX12882562,SRS10825219,SRA1320685,GEO,huazhong agricultural university,2,0.9349,0.92939,0.01147,0.01123,0.85488,0.85687,0.69455,0.61732,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_droplet,10x,,China,2021-11-01,Juvenile,Juvenile,Muscle,Muscular System 66850,SRR16681982,SRX12882561,SRS10825215,SRP344071,PRJNA776888,Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts,GSE186957,Transcriptome Analysis,Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish,,pubmed:39741296,,runx2b / bulk RNA seq rep1,GSM5664297,,source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ,runx2b / bulk RNA seq rep1,Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample,muscle and IB,,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,,strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:runx2b / ,GSM5664297,GSM5664297: runx2b / bulk RNA seq rep1; Danio rerio; RNA Seq,GSM5664297,,1,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,GEO Accession:GSM5664297,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP344071,,loader:fastq load.py,MUT_1_60dpf.R1.fq MUT_1_60dpf.R2.fq,fastq fastq,6876053100.0,22920177.0,GSM5664297 r1,0:150 1:150,A:1683687632;C:1665466650;G:1862910858;T:1663971371;N:16589,150,150,,,1683687632,1665466650,1862910858,1663971371,16589,SRX12882561,SRS10825215,SRA1320685,GEO,huazhong agricultural university,2,0.9327,0.92802,0.01178,0.0113,0.84861,0.84987,0.62221,0.67729,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_droplet,10x,,China,2021-11-01,Juvenile,Juvenile,Muscle,Muscular System 66851,SRR16681981,SRX12882560,SRS10825214,SRP344071,PRJNA776888,Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts,GSE186957,Transcriptome Analysis,Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish,,pubmed:39741296,,runx2b+/+ bulk RNA seq rep3,GSM5664296,,source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type,runx2b+/+ bulk RNA seq rep3,Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample,muscle and IB,,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,,strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type,GSM5664296,GSM5664296: runx2b+/+ bulk RNA seq rep3; Danio rerio; RNA Seq,GSM5664296,,1,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,GEO Accession:GSM5664296,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP344071,,loader:fastq load.py,WT_3_60dpf.R1.fq WT_3_60dpf.R2.fq,fastq fastq,6834033900.0,22780113.0,GSM5664296 r1,0:150 1:150,A:1665713519;C:1660512523;G:1864685424;T:1643106338;N:16096,150,150,,,1665713519,1660512523,1864685424,1643106338,16096,SRX12882560,SRS10825214,SRA1320685,GEO,huazhong agricultural university,2,0.92969,0.92347,0.01017,0.01012,0.85807,0.86001,0.63698,0.67717,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_droplet,10x,,China,2021-11-01,Juvenile,Juvenile,Muscle,Muscular System 66852,SRR16681980,SRX12882559,SRS10825212,SRP344071,PRJNA776888,Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts,GSE186957,Transcriptome Analysis,Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish,,pubmed:39741296,,runx2b+/+ bulk RNA seq rep2,GSM5664295,,source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type,runx2b+/+ bulk RNA seq rep2,Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample,muscle and IB,,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,,strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type,GSM5664295,GSM5664295: runx2b+/+ bulk RNA seq rep2; Danio rerio; RNA Seq,GSM5664295,,1,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,GEO Accession:GSM5664295,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP344071,,loader:fastq load.py,WT_2_60dpf.R1.fq WT_2_60dpf.R2.fq,fastq fastq,7007750400.0,23359168.0,GSM5664295 r1,0:150 1:150,A:1714498514;C:1702913716;G:1897215939;T:1693105532;N:16699,150,150,,,1714498514,1702913716,1897215939,1693105532,16699,SRX12882559,SRS10825212,SRA1320685,GEO,huazhong agricultural university,2,0.93182,0.92608,0.01221,0.01171,0.8478,0.85023,0.67158,0.65917,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_droplet,10x,,China,2021-11-01,Juvenile,Juvenile,Muscle,Muscular System 66853,SRR16681979,SRX12882558,SRS10825213,SRP344071,PRJNA776888,Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts,GSE186957,Transcriptome Analysis,Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation which potentially provides a basis for breeding strains of fish without xxx to improve the safe consumption and economic value of many aquaculture species and in this way boost the proportion of fish for the supply of animal protein worldwide Fig. 6. For this reason we needed to verify that the content of fatty acid in the runx2b / mutant was higher than that in runx2b+/+ fish as well as the expression of key genes related to IBs in the runx2b / and runx2b+/+ strains obtained by scRNA seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA seq and bulk seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish,,pubmed:39741296,,runx2b+/+ bulk RNA seq rep1,GSM5664294,,source name:muscle and IB|strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type,runx2b+/+ bulk RNA seq rep1,Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample,muscle and IB,,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,,strain:Tg sp7/eGFP transgenic line|tissue:muscle and IB|age:60 dpf|genotype:wild type,GSM5664294,GSM5664294: runx2b+/+ bulk RNA seq rep1; Danio rerio; RNA Seq,GSM5664294,,1,tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.,GEO Accession:GSM5664294,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP344071,,loader:fastq load.py,WT_1_60dpf.R1.fq WT_1_60dpf.R2.fq,fastq fastq,6785203800.0,22617346.0,GSM5664294 r1,0:150 1:150,A:1660992152;C:1637869425;G:1843210897;T:1643114944;N:16382,150,150,,,1660992152,1637869425,1843210897,1643114944,16382,SRX12882558,SRS10825213,SRA1320685,GEO,huazhong agricultural university,2,0.92763,0.92196,0.00968,0.00949,0.84295,0.84593,0.65456,0.65914,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_droplet,10x,,China,2021-11-01,Juvenile,Juvenile,Muscle,Muscular System