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31 rows where devstage_curation_coarse = "Embryo" and tissue_curation_coarse = "Muscular System"

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devstage_curation 6

technology 3

experiment.platform 2

experiment.library_selection 2

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tissue_curation_coarse 1

  • Muscular System · 31 ✖

tissue_curation 1

experiment.library_strategy 1

experiment.library_source 1

devstage_curation_coarse 1

  • Embryo · 31 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
34963 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.       Iso Seq RNA from embryo zero hpf C2 F2 6   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                 Iso Seq RNA from embyo 6 hpf C2 F2 6 C2 F2 6 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Gastrula Embryo Muscle Muscular System
34966 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.       Iso Seq RNA from embryo zero hpf C2 F2 24   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                 Iso Seq RNA from embyo 24 hpf C2 F2 24 C2 F2 24 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Pharyngula Embryo Muscle Muscular System
34977 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.       Iso Seq RNA from embryo zero hpf C2 F2 12   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                 Iso Seq RNA from embyo 12 hpf C2 F2 12 C2 F2 12 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Segmentation Embryo Muscle Muscular System
34978 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.       Iso Seq RNA from embryo zero hpf C2 F2 0   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                 Iso Seq RNA from embyo 0 hpf C2 F2 0 C2 F2 0 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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   0.00473   0.80371   0.50925   1489   T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Zygote Embryo Muscle Muscular System
36665 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.   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   strain:Tubingen|label:PE: paired end SE: single end|development stage:muscle                 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.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 1000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     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       872717534 808774955 1036781008 777391447 10908806 SRX257154 SRS405708 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.61428   0.09813   0.89305   0.6908   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-05-07 Undetermined Embryo Muscle Muscular System
47641 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.   pubmed:33343615   RLT rep3 GSM3029086   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’ ends of the reads and the trimmed reads were filtered with read length ≥ 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’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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C 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   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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029086 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     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     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   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47642 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.   pubmed:33343615   RLT rep2 GSM3029085   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’ ends of the reads and the trimmed reads were filtered with read length ≥ 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’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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C 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   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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029085 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     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     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   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47643 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.   pubmed:33343615   RLT rep1 GSM3029084   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’ ends of the reads and the trimmed reads were filtered with read length ≥ 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’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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C 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   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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029084 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     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     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   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47644 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.   pubmed:33343615   WT rep3 GSM3029083   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’ ends of the reads and the trimmed reads were filtered with read length ≥ 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’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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C 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   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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029083 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     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     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   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47645 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.   pubmed:33343615   WT rep2 GSM3029082   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’ ends of the reads and the trimmed reads were filtered with read length ≥ 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’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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C 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   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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029082 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     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     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   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47646 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.   pubmed:33343615   WT rep1 GSM3029081   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’ ends of the reads and the trimmed reads were filtered with read length ≥ 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’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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C 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   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（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029081 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     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     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   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
53013 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.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq Muscle rep2 GSM3934894   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   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® 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 ng 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   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® 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 ng 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   SRP213938     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     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   United States 2019-07-09 Pharyngula Embryo Muscle Muscular System
53014 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.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq Muscle rep1 GSM3934893   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   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® 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 ng 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   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® 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 ng 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   SRP213938     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     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   United States 2019-07-09 Pharyngula Embryo Muscle Muscular System
56291 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.       Zebrafish DMSO Rep 3 GSM4274800   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:DMSO GSM4274800 GSM4274800: Zebrafish DMSO Rep 3; Danio rerio; RNA Seq GSM4274800   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
56292 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.       Zebrafish DMSO Rep 2 GSM4274799   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:DMSO GSM4274799 GSM4274799: Zebrafish DMSO Rep 2; Danio rerio; RNA Seq GSM4274799   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
56293 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.       Zebrafish DMSO Rep 1 GSM4274798   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:DMSO GSM4274798 GSM4274798: Zebrafish DMSO Rep 1; Danio rerio; RNA Seq GSM4274798   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
56294 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.       Zebrafish NFA Rep 3 GSM4274797   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:NFA GSM4274797 GSM4274797: Zebrafish NFA Rep 3; Danio rerio; RNA Seq GSM4274797   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
56295 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.       Zebrafish NFA Rep 2 GSM4274796   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:NFA GSM4274796 GSM4274796: Zebrafish NFA Rep 2; Danio rerio; RNA Seq GSM4274796   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
56296 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.       Zebrafish NFA Rep 1 GSM4274795   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:NFA GSM4274795 GSM4274795: Zebrafish NFA Rep 1; Danio rerio; RNA Seq GSM4274795   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
56297 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.       Zebrafish LPA Rep 3 GSM4274794   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:LPA GSM4274794 GSM4274794: Zebrafish LPA Rep 3; Danio rerio; RNA Seq GSM4274794   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
56298 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.       Zebrafish LPA Rep 2 GSM4274793   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:LPA GSM4274793 GSM4274793: Zebrafish LPA Rep 2; Danio rerio; RNA Seq GSM4274793   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
56299 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.       Zebrafish LPA Rep 1 GSM4274792   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°C 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’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s 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°C without xxx for 48 hours. cell type:myogenic progenitor cells|treatment:LPA GSM4274792 GSM4274792: Zebrafish LPA Rep 1; Danio rerio; RNA Seq GSM4274792   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   SRP242229     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     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   United States 2020-01-16 Undetermined Embryo Muscle Muscular System
70269 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.   pubmed:36656711   Dr D952 muscle GSM6239391   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP379972   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     3626008907 3276288577 3379704474 3741159007 10855451 SRX15691883 SRS13388284     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   United States 2022-06-13 Undetermined Embryo Muscle Muscular System
70270 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.   pubmed:36656711   Dr D951 muscle GSM6239390   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP379972   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     3071420513 2643075340 2733408804 3130418227 8713085 SRX15691882 SRS13388283     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   United States 2022-06-13 Undetermined Embryo Muscle Muscular System
70271 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.   pubmed:36656711   Dr D950 muscle GSM6239389   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP379972   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     2767403244 2295939873 2397017404 2865891007 13419944 SRX15691881 SRS13388282     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   United States 2022-06-13 Undetermined Embryo Muscle Muscular System
70272 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.   pubmed:36656711   Dr D949 muscle GSM6239388   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP379972   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     3176604450 2731949532 2854109626 3290212961 9379974 SRX15691880 SRS13388281     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   United States 2022-06-13 Undetermined Embryo Muscle Muscular System
70273 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.   pubmed:36656711   Dr D948 muscle GSM6239387   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP379972   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     3544034201 2872687750 2988731712 3601227605 4920850 SRX15691879 SRS13388280     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   United States 2022-06-13 Undetermined Embryo Muscle Muscular System
70274 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.   pubmed:36656711   Dr Muscle3 GSM6239386   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP379972     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     564768913 546327011 532582494 559523522 460732 SRX15691878 SRS13388279     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   United States 2022-06-13 Undetermined Embryo Muscle Muscular System
70275 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.   pubmed:36656711   Dr Muscle2 GSM6239385   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP379972     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     646598229 592770801 584212215 625999341 508374 SRX15691877 SRS13388278     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   United States 2022-06-13 Undetermined Embryo Muscle Muscular System
71456 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.       Slow twitch Muscle tgPACPrdm1a:eGFP Sample2 GSM6592891   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP398129   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     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   United States 2022-09-19 Pharyngula Embryo Muscle Muscular System
71458 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.       Slow twitch Muscle tgPACPrdm1a:eGFP Sample1 GSM6592889   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP398129   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     4422627777 4011278190 6496127381 4190045039 2919785 SRX17631559 SRS15166362 SRA1501497 Lencer Laboratory, Department of Biology, Lafayette College Lencer Laboratory, Department of Biology, Lafayette College 2 0.91304 0.90702 0.10612 0.10501 0.77242 0.77415 0.52048 0.51584 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq bulk bulk bulk   United States 2022-09-19 Pharyngula Embryo Muscle Muscular System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;