{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and tissue_curation_coarse = \"Muscular System\"", "rows": [[34963, "SRR32588720", "SRX27895231", "SRS24266232", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 6", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 6 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 6 hpf", "C2 F2 6", "C2 F2 6", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231108_155338.hifi_reads.flnc.fastq.gz", "fastq", 6758669497.0, 3269612.0, "m54313U 231108 155338.hifi reads.flnc.fastq.gz", "0:2067.12", "A:1903955333;C:1520080315;G:1594879456;T:1739754393;N:0", 2067, null, null, null, 1903955333, 1520080315, 1594879456, 1739754393, 0, "SRX27895231", "SRS24266232", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Gastrula", "Embryo", "Muscle", "Muscular System"], [34966, "SRR32588723", "SRX27895228", "SRS24266230", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 24", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 24 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 24 hpf", "C2 F2 24", "C2 F2 24", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231109_165320.hifi_reads.flnc.fastq.gz", "fastq", 7642144881.0, 3850910.0, "m54313U 231109 165320.hifi reads.flnc.fastq.gz", "0:1984.50", "A:2137607023;C:1720821414;G:1812220379;T:1971496065;N:0", 1984, null, null, null, 2137607023, 1720821414, 1812220379, 1971496065, 0, "SRX27895228", "SRS24266230", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Pharyngula", "Embryo", "Muscle", "Muscular System"], [34977, "SRR32588734", "SRX27895217", "SRS24266222", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 12", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 12 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 12 hpf", "C2 F2 12", "C2 F2 12", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231111_191642.hifi_reads.flnc.fastq.gz", "fastq", 7627931284.0, 3897936.0, "m54313U 231111 191642.hifi reads.flnc.fastq.gz", "0:1956.92", "A:2146633241;C:1706673950;G:1799625470;T:1974998623;N:0", 1956, null, null, null, 2146633241, 1706673950, 1799625470, 1974998623, 0, "SRX27895217", "SRS24266222", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Segmentation", "Embryo", "Muscle", "Muscular System"], [34978, "SRR32588735", "SRX27895216", "SRS24266218", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 0", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 0 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 0 hpf", "C2 F2 0", "C2 F2 0", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231110_180503.hifi_reads.flnc.fastq.gz", "fastq", 8144050440.0, 3744842.0, "m54313U 231110 180503.hifi reads.flnc.fastq.gz", "0:2174.74", "A:2267401658;C:1836982566;G:1935470734;T:2104195482;N:0", 2174, null, null, null, 2267401658, 1836982566, 1935470734, 2104195482, 0, "SRX27895216", "SRS24266218", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", 1, 0.76793, null, 0.00473, null, 0.80371, null, 0.50925, null, 1489, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Zygote", "Embryo", "Muscle", "Muscular System"], [36665, "SRR800045", "SRX257154", "SRS405708", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "muscle RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end SE: single end|development stage:muscle", null, null, null, null, null, null, null, null, "muscle RNAseq totalRNARibominus", "muscle RNAseq totalRNARibominus", "9084X1", "Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 1000", "500Application ReadForward1", "SRP020008", null, null, "muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz", "Illumina native", 3506573750.0, 70131475.0, "9084X1 120420 SN141 0500 AD0TG5ACXX 5", "0:50", "A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806", 50, null, null, null, 872717534, 808774955, 1036781008, 777391447, 10908806, "SRX257154", "SRS405708", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.61428, null, 0.09813, null, 0.89305, null, 0.6908, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-05-07", "Undetermined", "Embryo", "Muscle", "Muscular System"], [47641, "SRR6798780", "SRX3757617", "SRS3013125", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep3", "GSM3029086", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep3", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029086", "GSM3029086: RLT rep3; Danio rerio; RNA Seq", "GSM3029086", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029086", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT3_1.fq.gz WT3_2.fq.gz", "fastq fastq", 8153906700.0, 27179689.0, "GSM3029086 r1", "0:150 1:150", "A:1876474081;C:2211352217;G:2118339495;T:1947510591;N:230316", 150, 150, null, null, 1876474081, 2211352217, 2118339495, 1947510591, 230316, "SRX3757617", "SRS3013125", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.93476, 0.93504, 0.13893, 0.13499, 0.82913, 0.83487, 0.53361, 0.54372, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47642, "SRR6798779", "SRX3757616", "SRS3013124", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep2", "GSM3029085", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep2", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029085", "GSM3029085: RLT rep2; Danio rerio; RNA Seq", "GSM3029085", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT2_1.fq.gz WT2_2.fq.gz", "fastq fastq", 7278822000.0, 24262740.0, "GSM3029085 r1", "0:150 1:150", "A:1623249687;C:2023479004;G:1940623122;T:1691262512;N:207675", 150, 150, null, null, 1623249687, 2023479004, 1940623122, 1691262512, 207675, "SRX3757616", "SRS3013124", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.94445, 0.94327, 0.112, 0.10647, 0.83591, 0.84226, 0.5112, 0.52155, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47643, "SRR6798778", "SRX3757615", "SRS3013123", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep1", "GSM3029084", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep1", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029084", "GSM3029084: RLT rep1; Danio rerio; RNA Seq", "GSM3029084", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029084", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT1_1.fq.gz WT1_2.fq.gz", "fastq fastq", 8127579000.0, 27091930.0, "GSM3029084 r1", "0:150 1:150", "A:1936609330;C:2121138923;G:2083423270;T:1986178311;N:229166", 150, 150, null, null, 1936609330, 2121138923, 2083423270, 1986178311, 229166, "SRX3757615", "SRS3013123", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.66403, 0.66289, 0.14695, 0.14227, 0.82503, 0.82958, 0.54774, 0.55661, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47644, "SRR6798777", "SRX3757614", "SRS3013122", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep3", "GSM3029083", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep3", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029083", "GSM3029083: WT rep3; Danio rerio; RNA Seq", "GSM3029083", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT3_1.fq.gz RLT3_2.fq.gz", "fastq fastq", 7458295500.0, 24860985.0, "GSM3029083 r1", "0:150 1:150", "A:1875422371;C:1858400851;G:1819493497;T:1904874518;N:104263", 150, 150, null, null, 1875422371, 1858400851, 1819493497, 1904874518, 104263, "SRX3757614", "SRS3013122", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.88642, 0.88696, 0.1881, 0.18533, 0.79537, 0.80073, 0.50351, 0.48568, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47645, "SRR6798776", "SRX3757613", "SRS3013120", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep2", "GSM3029082", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep2", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029082", "GSM3029082: WT rep2; Danio rerio; RNA Seq", "GSM3029082", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT2_2.fq.gz RLT2_1.fq.gz", "fastq fastq", 9462767100.0, 31542557.0, "GSM3029082 r1", "0:150 1:150", "A:2301678607;C:2445064584;G:2361534540;T:2354357373;N:131996", 150, 150, null, null, 2301678607, 2445064584, 2361534540, 2354357373, 131996, "SRX3757613", "SRS3013120", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.91337, 0.91337, 0.17924, 0.17526, 0.78317, 0.79011, 0.50203, 0.51647, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47646, "SRR6798775", "SRX3757612", "SRS3013121", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep1", "GSM3029081", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep1", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029081", "GSM3029081: WT rep1; Danio rerio; RNA Seq", "GSM3029081", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT1_1.fq.gz RLT1_2.fq.gz", "fastq fastq", 7599797400.0, 25332658.0, "GSM3029081 r1", "0:150 1:150", "A:1883972109;C:1921348946;G:1869717767;T:1924652451;N:106127", 150, 150, null, null, 1883972109, 1921348946, 1869717767, 1924652451, 106127, "SRX3757612", "SRS3013121", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.88692, 0.88623, 0.18432, 0.18166, 0.79928, 0.80693, 0.50362, 0.5124, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [53013, "SRR9662026", "SRX6422902", "SRS5079692", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA Seq Muscle rep2", "GSM3934894", null, "source name:Tissue|strain:Tuebingen|tissue:Muscle", "YueLab RNA Seq Muscle rep2", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "Tissue", null, "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Muscle", "GSM3934894", "GSM3934894: YueLab RNA Seq Muscle rep2; Danio rerio; RNA Seq", "GSM3934894", null, "1", "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "GEO Accession:GSM3934894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-Muscle-rep2_1.fastq.gz YueLab-RNA-Seq-Muscle-rep2_2.fastq.gz", "fastq fastq", 2021185692.0, 19815546.0, "GSM3934894 r1", "0:51 1:51", "A:508251350;C:473502441;G:462707891;T:537489259;N:39234751", 51, 51, null, null, 508251350, 473502441, 462707891, 537489259, 39234751, "SRX6422902", "SRS5079692", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.94958, 0.95251, 0.06157, 0.05992, 0.77398, 0.77802, 0.50205, 0.53541, 51, 51, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Muscle", "Muscular System"], [53014, "SRR9662025", "SRX6422901", "SRS5079691", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA Seq Muscle rep1", "GSM3934893", null, "source name:Tissue|strain:Tuebingen|tissue:Muscle", "YueLab RNA Seq Muscle rep1", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "Tissue", null, "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Muscle", "GSM3934893", "GSM3934893: YueLab RNA Seq Muscle rep1; Danio rerio; RNA Seq", "GSM3934893", null, "1", "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "GEO Accession:GSM3934893", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-Muscle-rep1_1.fastq.gz YueLab-RNA-Seq-Muscle-rep1_2.fastq.gz", "fastq fastq", 3952674128.0, 32728471.0, "GSM3934893 r1", "0:60.49 1:60.28", "A:1031292985;C:933897200;G:906173487;T:1081251504;N:58952", 60, 60, null, null, 1031292985, 933897200, 906173487, 1081251504, 58952, "SRX6422901", "SRS5079691", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.98113, 0.98146, 0.05897, 0.05792, 0.77973, 0.78374, 0.56016, 0.55409, 61, 60, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Muscle", "Muscular System"], [56291, "SRR10903545", "SRX7571714", "SRS6007290", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 3", "GSM4274800", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 3", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274800", "GSM4274800: Zebrafish DMSO Rep 3; Danio rerio; RNA Seq", "GSM4274800", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274800", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z3_S3_R2_001.fastq.gz DMSO-Z3_S3_R1_001.fastq.gz", "fastq fastq", 3131766552.0, 41732800.0, "GSM4274800 r1", "0:37.52 1:37.52", "A:885347014;C:656593900;G:658966405;T:930204699;N:654534", 37, 37, null, null, 885347014, 656593900, 658966405, 930204699, 654534, "SRX7571714", "SRS6007290", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.9017, 0.90284, 0.20295, 0.20352, 0.726, 0.72681, 0.4835, 0.48166, 37, 36, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56292, "SRR10903544", "SRX7571713", "SRS6007289", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 2", "GSM4274799", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 2", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274799", "GSM4274799: Zebrafish DMSO Rep 2; Danio rerio; RNA Seq", "GSM4274799", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274799", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z2_S2_R2_001.fastq.gz DMSO-Z2_S2_R1_001.fastq.gz", "fastq fastq", 3602763184.0, 48016122.0, "GSM4274799 r1", "0:37.52 1:37.52", "A:1036072046;C:737502030;G:741972436;T:1086457828;N:758844", 37, 37, null, null, 1036072046, 737502030, 741972436, 1086457828, 758844, "SRX7571713", "SRS6007289", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89788, 0.8998, 0.22198, 0.22328, 0.72324, 0.72612, 0.47822, 0.47673, 38, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56293, "SRR10903543", "SRX7571712", "SRS6007288", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 1", "GSM4274798", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 1", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274798", "GSM4274798: Zebrafish DMSO Rep 1; Danio rerio; RNA Seq", "GSM4274798", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z1_S1_R2_001.fastq.gz DMSO-Z1_S1_R1_001.fastq.gz", "fastq fastq", 3604342960.0, 48032922.0, "GSM4274798 r1", "0:37.52 1:37.52", "A:1012371470;C:761879249;G:766369377;T:1062980320;N:742544", 37, 37, null, null, 1012371470, 761879249, 766369377, 1062980320, 742544, "SRX7571712", "SRS6007288", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90147, 0.90411, 0.18135, 0.18178, 0.72756, 0.72989, 0.48286, 0.484, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56294, "SRR10903542", "SRX7571711", "SRS6007287", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 3", "GSM4274797", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 3", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274797", "GSM4274797: Zebrafish NFA Rep 3; Danio rerio; RNA Seq", "GSM4274797", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274797", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z3_S9_R2_001.fastq.gz NFA-Z3_S9_R1_001.fastq.gz", "fastq fastq", 2585502086.0, 34448695.0, "GSM4274797 r1", "0:37.53 1:37.53", "A:703025617;C:569504763;G:571097453;T:741333725;N:540528", 37, 37, null, null, 703025617, 569504763, 571097453, 741333725, 540528, "SRX7571711", "SRS6007287", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90534, 0.90734, 0.17389, 0.17443, 0.72569, 0.72689, 0.47635, 0.47915, 36, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56295, "SRR10903541", "SRX7571710", "SRS6007286", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 2", "GSM4274796", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 2", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274796", "GSM4274796: Zebrafish NFA Rep 2; Danio rerio; RNA Seq", "GSM4274796", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z2_S8_R2_001.fastq.gz NFA-Z2_S8_R1_001.fastq.gz", "fastq fastq", 3166928712.0, 42208361.0, "GSM4274796 r1", "0:37.52 1:37.52", "A:922958966;C:638285887;G:640244924;T:964802852;N:636083", 37, 37, null, null, 922958966, 638285887, 640244924, 964802852, 636083, "SRX7571710", "SRS6007286", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.8974, 0.89826, 0.21803, 0.21778, 0.72679, 0.72825, 0.48119, 0.48197, 37, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56296, "SRR10903540", "SRX7571709", "SRS6007285", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 1", "GSM4274795", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 1", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274795", "GSM4274795: Zebrafish NFA Rep 1; Danio rerio; RNA Seq", "GSM4274795", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z1_S7_R2_001.fastq.gz NFA-Z1_S7_R1_001.fastq.gz", "fastq fastq", 2962555966.0, 39481568.0, "GSM4274795 r1", "0:37.52 1:37.52", "A:850455036;C:607610800;G:611012952;T:892860213;N:616965", 37, 37, null, null, 850455036, 607610800, 611012952, 892860213, 616965, "SRX7571709", "SRS6007285", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89392, 0.89571, 0.25628, 0.25686, 0.72153, 0.72297, 0.47614, 0.47823, 38, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56297, "SRR10903539", "SRX7571708", "SRS6007284", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 3", "GSM4274794", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 3", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274794", "GSM4274794: Zebrafish LPA Rep 3; Danio rerio; RNA Seq", "GSM4274794", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274794", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "LPA-Z3_S6_R2_001.fastq.gz LPA-Z3_S6_R1_001.fastq.gz", "fastq fastq", 3066652967.0, 40865355.0, "GSM4274794 r1", "0:37.52 1:37.52", "A:864150135;C:645040202;G:648074884;T:908748285;N:639461", 37, 37, null, null, 864150135, 645040202, 648074884, 908748285, 639461, "SRX7571708", "SRS6007284", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89879, 0.89988, 0.21861, 0.21824, 0.72705, 0.72953, 0.47984, 0.48124, 36, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56298, "SRR10903538", "SRX7571707", "SRS6007283", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 2", "GSM4274793", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 2", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274793", "GSM4274793: Zebrafish LPA Rep 2; Danio rerio; RNA Seq", "GSM4274793", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274793", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "LPA-Z2_S5_R2_001.fastq.gz LPA-Z2_S5_R1_001.fastq.gz", "fastq fastq", 3259713731.0, 43430992.0, "GSM4274793 r1", "0:37.53 1:37.53", "A:889586274;C:714766857;G:716243885;T:938441843;N:674872", 37, 37, null, null, 889586274, 714766857, 716243885, 938441843, 674872, "SRX7571707", "SRS6007283", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90057, 0.90315, 0.2034, 0.20364, 0.72583, 0.72819, 0.48128, 0.48201, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56299, "SRR10903537", "SRX7571706", "SRS6007282", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 1", "GSM4274792", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 1", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274792", "GSM4274792: Zebrafish LPA Rep 1; Danio rerio; RNA Seq", "GSM4274792", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274792", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "LPA-Z1_S4_R2_001.fastq.gz LPA-Z1_S4_R1_001.fastq.gz", "fastq fastq", 2616479059.0, 34861517.0, "GSM4274792 r1", "0:37.53 1:37.53", "A:703413035;C:586630572;G:585887430;T:740028263;N:519759", 37, 37, null, null, 703413035, 586630572, 585887430, 740028263, 519759, "SRX7571706", "SRS6007282", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.9153, 0.91479, 0.15809, 0.1583, 0.72936, 0.73064, 0.48034, 0.46478, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70269, "SRR19641871", "SRX15691883", "SRS13388284", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D952 muscle", "GSM6239391", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D952 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239391", "GSM6239391: Dr D952 muscle; Danio rerio; RNA Seq", "GSM6239391 r1", "GSM6239391", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D952_Muscle.R1.fastq.gz D952_Muscle.R2.fastq.gz", "fastq fastq", 14034016416.0, 92998913.0, "GSM6239391 r1", "0:75.51 1:75.40", "A:3626008907;C:3276288577;G:3379704474;T:3741159007;N:10855451", 75, 75, null, null, 3626008907, 3276288577, 3379704474, 3741159007, 10855451, "SRX15691883", "SRS13388284", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.97042, 0.97347, 0.07223, 0.04214, 0.82538, 0.82927, 0.55476, 0.56579, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70270, "SRR19641872", "SRX15691882", "SRS13388283", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D951 muscle", "GSM6239390", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D951 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239390", "GSM6239390: Dr D951 muscle; Danio rerio; RNA Seq", "GSM6239390 r1", "GSM6239390", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D951_Muscle.R1.fastq.gz D951_Muscle.R2.fastq.gz", "fastq fastq", 11587035969.0, 76778498.0, "GSM6239390 r1", "0:75.50 1:75.42", "A:3071420513;C:2643075340;G:2733408804;T:3130418227;N:8713085", 75, 75, null, null, 3071420513, 2643075340, 2733408804, 3130418227, 8713085, "SRX15691882", "SRS13388283", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.96746, 0.96774, 0.10063, 0.06529, 0.74819, 0.75444, 0.55536, 0.56065, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70271, "SRR19641879", "SRX15691881", "SRS13388282", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D950 muscle", "GSM6239389", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D950 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239389", "GSM6239389: Dr D950 muscle; Danio rerio; RNA Seq", "GSM6239389 r1", "GSM6239389", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D950_Muscle.R1.fastq.gz D950_Muscle.R2.fastq.gz", "fastq fastq", 10339671472.0, 68539957.0, "GSM6239389 r1", "0:75.42 1:75.44", "A:2767403244;C:2295939873;G:2397017404;T:2865891007;N:13419944", 75, 75, null, null, 2767403244, 2295939873, 2397017404, 2865891007, 13419944, "SRX15691881", "SRS13388282", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.97131, 0.97203, 0.0769, 0.04197, 0.82215, 0.82554, 0.61202, 0.621, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70272, "SRR19641873", "SRX15691880", "SRS13388281", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D949 muscle", "GSM6239388", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D949 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239388", "GSM6239388: Dr D949 muscle; Danio rerio; RNA Seq", "GSM6239388 r1", "GSM6239388", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D949_Muscle.R1.fastq.gz D949_Muscle.R2.fastq.gz", "fastq fastq", 12062256543.0, 79950635.0, "GSM6239388 r1", "0:75.49 1:75.39", "A:3176604450;C:2731949532;G:2854109626;T:3290212961;N:9379974", 75, 75, null, null, 3176604450, 2731949532, 2854109626, 3290212961, 9379974, "SRX15691880", "SRS13388281", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.96846, 0.97192, 0.07324, 0.04176, 0.81412, 0.81793, 0.57983, 0.58149, 74, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70273, "SRR19641874", "SRX15691879", "SRS13388280", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D948 muscle", "GSM6239387", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D948 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239387", "GSM6239387: Dr D948 muscle; Danio rerio; RNA Seq", "GSM6239387 r1", "GSM6239387", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D948_Muscle.R1.fastq.gz D948_Muscle.R2.fastq.gz", "fastq fastq", 13011602118.0, 86234782.0, "GSM6239387 r1", "0:75.47 1:75.41", "A:3544034201;C:2872687750;G:2988731712;T:3601227605;N:4920850", 75, 75, null, null, 3544034201, 2872687750, 2988731712, 3601227605, 4920850, "SRX15691879", "SRS13388280", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.96775, 0.97203, 0.07435, 0.04278, 0.81913, 0.83132, 0.55972, 0.63188, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70274, "SRR19641875", "SRX15691878", "SRS13388279", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr Muscle3", "GSM6239386", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:258 days|transgene:n1|cell line:n1|model:no transgene", "Dr Muscle3", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:258 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239386", "GSM6239386: Dr Muscle3; Danio rerio; RNA Seq", "GSM6239386 r1", "GSM6239386", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP379972", null, null, "A374-A375T24.R1.fastq.gz A374-A375T24.R2.fastq.gz", "fastq fastq", 2203662672.0, 21604536.0, "GSM6239386 r1", "0:51 1:51", "A:564768913;C:546327011;G:532582494;T:559523522;N:460732", 51, 51, null, null, 564768913, 546327011, 532582494, 559523522, 460732, "SRX15691878", "SRS13388279", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.83261, 0.82686, 0.07473, 0.06901, 0.80493, 0.80657, 0.49306, 0.49193, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70275, "SRR19641876", "SRX15691877", "SRS13388278", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr Muscle2", "GSM6239385", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:258 days|transgene:n1|cell line:n1|model:no transgene", "Dr Muscle2", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:258 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239385", "GSM6239385: Dr Muscle2; Danio rerio; RNA Seq", "GSM6239385 r1", "GSM6239385", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP379972", null, null, "A374-A375T23.R1.fastq.gz A374-A375T23.R2.fastq.gz", "fastq fastq", 2450088960.0, 24020480.0, "GSM6239385 r1", "0:51 1:51", "A:646598229;C:592770801;G:584212215;T:625999341;N:508374", 51, 51, null, null, 646598229, 592770801, 584212215, 625999341, 508374, "SRX15691877", "SRS13388278", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.9278, 0.92032, 0.09971, 0.09347, 0.80986, 0.81028, 0.51973, 0.52123, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [71456, "SRR21631159", "SRX17631561", "SRS15166364", "SRP398129", "PRJNA882122", "Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish", "GSE213728", "Transcriptome Analysis", "Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.", null, null, null, "Slow twitch Muscle tgPACPrdm1a:eGFP Sample2", "GSM6592891", null, "source name:slow twitch muscle|tissue:slow twitch muscle|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing", "Slow twitch Muscle tgPACPrdm1a:eGFP Sample2", "Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file", "slow twitch muscle", "For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf", "standard Illumina Kit for stranded RNAseq", "Embryos reared at 28C until 24hpf.", "tissue:slow twitch muscle|genotype:wildtype|treatment:n1", "GSM6592891", "GSM6592891: Slow twitch Muscle tgPACPrdm1a:eGFP Sample2; Danio rerio; RNA Seq", "GSM6592891 r1", "GSM6592891", "1", "standard Illumina Kit for stranded RNAseq", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP398129", null, "loader:fastq load.py", "Sample3_GFP_24hpf_S3_L002_R1_001.fastq.gz Sample3_GFP_24hpf_S3_L002_R2_001.fastq.gz", "fastq fastq", 19887469194.0, 65852547.0, "GSM6592891 r1", "0:151 1:151", "A:4595886435;C:4222799298;G:6711875529;T:4353875479;N:3032453", 151, 151, null, null, 4595886435, 4222799298, 6711875529, 4353875479, 3032453, "SRX17631561", "SRS15166364", "SRA1501497", "Lencer Laboratory, Department of Biology, Lafayette College", "Lencer Laboratory, Department of Biology, Lafayette College", 2, 0.92086, 0.91566, 0.10394, 0.10303, 0.75808, 0.76002, 0.51563, 0.51331, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2022-09-19", "Pharyngula", "Embryo", "Muscle", "Muscular System"], [71458, "SRR21631161", "SRX17631559", "SRS15166362", "SRP398129", "PRJNA882122", "Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish", "GSE213728", "Transcriptome Analysis", "Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100 prepared for stranded Illumina sequencing and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.", null, null, null, "Slow twitch Muscle tgPACPrdm1a:eGFP Sample1", "GSM6592889", null, "source name:slow twitch muscle|tissue:slow twitch muscle|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing", "Slow twitch Muscle tgPACPrdm1a:eGFP Sample1", "Read aligment with STAR counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file", "slow twitch muscle", "For cyclopamine treated samples embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf", "standard Illumina Kit for stranded RNAseq", "Embryos reared at 28C until 24hpf.", "tissue:slow twitch muscle|genotype:wildtype|treatment:n1", "GSM6592889", "GSM6592889: Slow twitch Muscle tgPACPrdm1a:eGFP Sample1; Danio rerio; RNA Seq", "GSM6592889 r1", "GSM6592889", "1", "standard Illumina Kit for stranded RNAseq", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP398129", null, "loader:fastq load.py", "Sample1_GFP_24hpf_S1_L002_R1_001.fastq.gz Sample1_GFP_24hpf_S1_L002_R2_001.fastq.gz", "fastq fastq", 19122998172.0, 63321186.0, "GSM6592889 r1", "0:151 1:151", "A:4422627777;C:4011278190;G:6496127381;T:4190045039;N:2919785", 151, 151, 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