{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and tissue_curation = \"Muscle\"", "rows": [[36665, "SRR800045", "SRX257154", "SRS405708", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "muscle RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end SE: single end|development stage:muscle", null, null, null, null, null, null, null, null, "muscle RNAseq totalRNARibominus", "muscle RNAseq totalRNARibominus", "9084X1", "Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 1000", "500Application ReadForward1", "SRP020008", null, null, "muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz", "Illumina native", 3506573750.0, 70131475.0, "9084X1 120420 SN141 0500 AD0TG5ACXX 5", "0:50", "A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806", 50, null, null, null, 872717534, 808774955, 1036781008, 777391447, 10908806, "SRX257154", "SRS405708", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.61428, null, 0.09813, null, 0.89305, null, 0.6908, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-05-07", "Undetermined", "Embryo", "Muscle", "Muscular System"], [49268, "SRR7883101", "SRX4721396", "SRS3806484", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT sample 3", "GSM3396896", null, "source name:Gr mutant swimming UOPT |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396896", "GSM3396896: Gr mutant swimming UOPT sample 3; Danio rerio; RNA Seq", "GSM3396896", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396896", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_15_15105_CTTGTA_L001_R1_001.fastq.gz", "fastq", 248411565.0, 4870815.0, "GSM3396896 r1", "0:51", "A:56574599;C:63639902;G:59333109;T:68728919;N:135036", 51, null, null, null, 56574599, 63639902, 59333109, 68728919, 135036, "SRX4721396", "SRS3806484", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95963, null, 0.03133, null, 0.82144, null, 0.50958, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49269, "SRR7883102", "SRX4721396", "SRS3806484", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT sample 3", "GSM3396896", null, "source name:Gr mutant swimming UOPT |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396896", "GSM3396896: Gr mutant swimming UOPT sample 3; Danio rerio; RNA Seq", "GSM3396896", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396896", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_15_15105_CTTGTA_L002_R1_001.fastq.gz", "fastq", 245868501.0, 4820951.0, "GSM3396896 r2", "0:51", "A:55999278;C:63022234;G:58753181;T:68048742;N:45066", 51, null, null, null, 55999278, 63022234, 58753181, 68048742, 45066, "SRX4721396", "SRS3806484", "SRA780034", "GEO", "ZF-screens BV", 1, 0.9607, null, 0.03061, null, 0.81876, null, 0.50656, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49270, "SRR7883099", "SRX4721395", "SRS3806483", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT sample 2", "GSM3396895", null, "source name:Gr mutant swimming UOPT |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396895", "GSM3396895: Gr mutant swimming UOPT sample 2; Danio rerio; RNA Seq", "GSM3396895", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396895", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_14_15104_CAGATC_L001_R1_001.fastq.gz", "fastq", 219513996.0, 4304196.0, "GSM3396895 r1", "0:51", "A:48361086;C:57271498;G:53468696;T:60291615;N:121101", 51, null, null, null, 48361086, 57271498, 53468696, 60291615, 121101, "SRX4721395", "SRS3806483", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95734, null, 0.02232, null, 0.83037, null, 0.46039, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49271, "SRR7883100", "SRX4721395", "SRS3806483", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT sample 2", "GSM3396895", null, "source name:Gr mutant swimming UOPT |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396895", "GSM3396895: Gr mutant swimming UOPT sample 2; Danio rerio; RNA Seq", "GSM3396895", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396895", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_14_15104_CAGATC_L002_R1_001.fastq.gz", "fastq", 217279176.0, 4260376.0, "GSM3396895 r2", "0:51", "A:47895589;C:56699017;G:52953041;T:59691639;N:39890", 51, null, null, null, 47895589, 56699017, 52953041, 59691639, 39890, "SRX4721395", "SRS3806483", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95882, null, 0.02375, null, 0.82753, null, 0.45523, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49272, "SRR7883095", "SRX4721394", "SRS3806482", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT sample 1", "GSM3396894", null, "source name:Gr mutant swimming UOPT |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396894", "GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq", "GSM3396894", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_11_14126_CGATGT_L001_R1_000.fastq.gz", "fastq", 76142847.0, 1492997.0, "GSM3396894 r1", "0:51", "A:17764968;C:19359482;G:17546237;T:21458644;N:13516", 51, null, null, null, 17764968, 19359482, 17546237, 21458644, 13516, "SRX4721394", "SRS3806482", "SRA780034", "GEO", "ZF-screens BV", 1, 0.94854, null, 0.03967, null, 0.81239, null, 0.52843, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49273, "SRR7883096", "SRX4721394", "SRS3806482", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT sample 1", "GSM3396894", null, "source name:Gr mutant swimming UOPT |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396894", "GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq", "GSM3396894", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_11_14126_CGATGT_L002_R1_000.fastq.gz", "fastq", 75245655.0, 1475405.0, "GSM3396894 r2", "0:51", "A:17559056;C:19128796;G:17344883;T:21206265;N:6655", 51, null, null, null, 17559056, 19128796, 17344883, 21206265, 6655, "SRX4721394", "SRS3806482", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95076, null, 0.03952, null, 0.81057, null, 0.52805, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49274, "SRR7883097", "SRX4721394", "SRS3806482", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT sample 1", "GSM3396894", null, "source name:Gr mutant swimming UOPT |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396894", "GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq", "GSM3396894", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_11_14126_CGATGT_L001_R1_001.fastq.gz", "fastq", 282942084.0, 5547884.0, "GSM3396894 r3", "0:51", "A:65346157;C:71914444;G:66015753;T:79625150;N:40580", 51, null, null, null, 65346157, 71914444, 66015753, 79625150, 40580, "SRX4721394", "SRS3806482", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95533, null, 0.03742, null, 0.81044, null, 0.52574, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49275, "SRR7883098", "SRX4721394", "SRS3806482", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT sample 1", "GSM3396894", null, "source name:Gr mutant swimming UOPT |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396894", "GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq", "GSM3396894", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_11_14126_CGATGT_L002_R1_001.fastq.gz", "fastq", 279101274.0, 5472574.0, "GSM3396894 r4", "0:51", "A:64447735;C:70937019;G:65137622;T:78531620;N:47278", 51, null, null, null, 64447735, 70937019, 65137622, 78531620, 47278, "SRX4721394", "SRS3806482", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95428, null, 0.03783, null, 0.81128, null, 0.52701, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49276, "SRR7883093", "SRX4721393", "SRS3806481", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 3", "GSM3396893", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396893", "GSM3396893: Wild type swimming UOPT++ sample 3; Danio rerio; RNA Seq", "GSM3396893", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396893", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_13_15103_GCCAAT_L001_R1_001.fastq.gz", "fastq", 354993966.0, 6960666.0, "GSM3396893 r1", "0:51", "A:84489335;C:86597253;G:84240000;T:99472362;N:195016", 51, null, null, null, 84489335, 86597253, 84240000, 99472362, 195016, "SRX4721393", "SRS3806481", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95532, null, 0.04239, null, 0.80653, null, 0.55623, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49277, "SRR7883094", "SRX4721393", "SRS3806481", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 3", "GSM3396893", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396893", "GSM3396893: Wild type swimming UOPT++ sample 3; Danio rerio; RNA Seq", "GSM3396893", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396893", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_13_15103_GCCAAT_L002_R1_001.fastq.gz", "fastq", 351290193.0, 6888043.0, "GSM3396893 r2", "0:51", "A:83629618;C:85716733;G:83395630;T:98483376;N:64836", 51, null, null, null, 83629618, 85716733, 83395630, 98483376, 64836, "SRX4721393", "SRS3806481", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95631, null, 0.04199, null, 0.8056, null, 0.54571, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49278, "SRR7883089", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L001_R1_000.fastq.gz", "fastq", 70889949.0, 1389999.0, "GSM3396892 r1", "0:51", "A:16926874;C:17543094;G:16728407;T:19679197;N:12377", 51, null, null, null, 16926874, 17543094, 16728407, 19679197, 12377, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95627, null, 0.03548, null, 0.82451, null, 0.53415, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49279, "SRR7883090", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L002_R1_000.fastq.gz", "fastq", 70218126.0, 1376826.0, "GSM3396892 r2", "0:51", "A:16757913;C:17378481;G:16577230;T:19498501;N:6001", 51, null, null, null, 16757913, 17378481, 16577230, 19498501, 6001, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95571, null, 0.03554, null, 0.82806, null, 0.50999, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49280, "SRR7883091", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L001_R1_001.fastq.gz", "fastq", 276251241.0, 5416691.0, "GSM3396892 r3", "0:51", "A:65379164;C:68332333;G:65926683;T:76572534;N:40527", 51, null, null, null, 65379164, 68332333, 65926683, 76572534, 40527, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.96013, null, 0.0352, null, 0.82814, null, 0.53974, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49281, "SRR7883092", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L002_R1_001.fastq.gz", "fastq", 273560328.0, 5363928.0, "GSM3396892 r4", "0:51", "A:64737712;C:67666247;G:65306231;T:75803211;N:46927", 51, null, null, null, 64737712, 67666247, 65306231, 75803211, 46927, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95941, null, 0.03355, null, 0.82745, null, 0.54235, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49282, "SRR7883087", "SRX4721391", "SRS3806479", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 1", "GSM3396891", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396891", "GSM3396891: Wild type swimming UOPT++ sample 1; Danio rerio; RNA Seq", "GSM3396891", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396891", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_08_14124_CGTACG_L001_R1_001.fastq.gz", "fastq", 391510986.0, 7676686.0, "GSM3396891 r1", "0:51", "A:93242107;C:96684654;G:92114654;T:109292193;N:177378", 51, null, null, null, 93242107, 96684654, 92114654, 109292193, 177378, "SRX4721391", "SRS3806479", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95344, null, 0.05682, null, 0.80612, null, 0.46874, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49283, "SRR7883088", "SRX4721391", "SRS3806479", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 1", "GSM3396891", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396891", "GSM3396891: Wild type swimming UOPT++ sample 1; Danio rerio; RNA Seq", "GSM3396891", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396891", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_08_14124_CGTACG_L002_R1_001.fastq.gz", "fastq", 387065571.0, 7589521.0, "GSM3396891 r2", "0:51", "A:92211053;C:95616109;G:91125664;T:108078262;N:34483", 51, null, null, null, 92211053, 95616109, 91125664, 108078262, 34483, "SRX4721391", "SRS3806479", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95555, null, 0.05726, null, 0.80655, null, 0.50316, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49284, "SRR7883085", "SRX4721390", "SRS3806478", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST sample 3", "GSM3396890", null, "source name:Gr mutant resting REST |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396890", "GSM3396890: Gr mutant resting REST sample 3; Danio rerio; RNA Seq", "GSM3396890", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396890", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_06_14123_GTTTCG_L001_R1_001.fastq.gz", "fastq", 402333798.0, 7888898.0, "GSM3396890 r1", "0:51", "A:93056953;C:102519574;G:95945518;T:110623659;N:188094", 51, null, null, null, 93056953, 102519574, 95945518, 110623659, 188094, "SRX4721390", "SRS3806478", "SRA780034", "GEO", "ZF-screens BV", 1, 0.96072, null, 0.03044, null, 0.83151, null, 0.49904, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49285, "SRR7883086", "SRX4721390", "SRS3806478", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST sample 3", "GSM3396890", null, "source name:Gr mutant resting REST |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396890", "GSM3396890: Gr mutant resting REST sample 3; Danio rerio; RNA Seq", "GSM3396890", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396890", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_06_14123_GTTTCG_L002_R1_001.fastq.gz", "fastq", 397844166.0, 7800866.0, "GSM3396890 r2", "0:51", "A:92045457;C:101410388;G:94956743;T:109396044;N:35534", 51, null, null, null, 92045457, 101410388, 94956743, 109396044, 35534, "SRX4721390", "SRS3806478", "SRA780034", "GEO", "ZF-screens BV", 1, 0.96026, null, 0.03027, null, 0.82994, null, 0.49932, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49286, "SRR7883083", "SRX4721389", "SRS3806477", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST sample 2", "GSM3396889", null, "source name:Gr mutant resting REST |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396889", "GSM3396889: Gr mutant resting REST sample 2; Danio rerio; RNA Seq", "GSM3396889", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396889", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_05_14122_GTGGCC_L001_R1_001.fastq.gz", "fastq", 415265307.0, 8142457.0, "GSM3396889 r1", "0:51", "A:96524820;C:105111599;G:96647633;T:116788874;N:192381", 51, null, null, null, 96524820, 105111599, 96647633, 116788874, 192381, "SRX4721389", "SRS3806477", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95102, null, 0.04156, null, 0.79164, null, 0.52657, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49287, "SRR7883084", "SRX4721389", "SRS3806477", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST sample 2", "GSM3396889", null, "source name:Gr mutant resting REST |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396889", "GSM3396889: Gr mutant resting REST sample 2; Danio rerio; RNA Seq", "GSM3396889", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396889", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_05_14122_GTGGCC_L002_R1_001.fastq.gz", "fastq", 410798625.0, 8054875.0, "GSM3396889 r2", "0:51", "A:95514290;C:104001536;G:95684811;T:115561454;N:36534", 51, null, null, null, 95514290, 104001536, 95684811, 115561454, 36534, "SRX4721389", "SRS3806477", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95117, null, 0.04146, null, 0.79032, null, 0.51379, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49288, "SRR7883081", "SRX4721388", "SRS3806476", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST sample 1", "GSM3396888", null, "source name:Gr mutant resting REST |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396888", "GSM3396888: Gr mutant resting REST sample 1; Danio rerio; RNA Seq", "GSM3396888", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396888", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_04_14121_GGCTAC_L001_R1_001.fastq.gz", "fastq", 356273607.0, 6985757.0, "GSM3396888 r1", "0:51", "A:83067213;C:89144746;G:86927052;T:96973321;N:161275", 51, null, null, null, 83067213, 89144746, 86927052, 96973321, 161275, "SRX4721388", "SRS3806476", "SRA780034", "GEO", "ZF-screens BV", 1, 0.9514, null, 0.03636, null, 0.78064, null, 0.49277, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49289, "SRR7883082", "SRX4721388", "SRS3806476", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST sample 1", "GSM3396888", null, "source name:Gr mutant resting REST |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396888", "GSM3396888: Gr mutant resting REST sample 1; Danio rerio; RNA Seq", "GSM3396888", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396888", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_04_14121_GGCTAC_L002_R1_001.fastq.gz", "fastq", 353427042.0, 6929942.0, "GSM3396888 r2", "0:51", "A:82429330;C:88444066;G:86279627;T:96242734;N:31285", 51, null, null, null, 82429330, 88444066, 86279627, 96242734, 31285, "SRX4721388", "SRS3806476", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95127, null, 0.03685, null, 0.78125, null, 0.49716, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49290, "SRR7883079", "SRX4721387", "SRS3806475", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 3", "GSM3396887", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396887", "GSM3396887: Wild type resting REST++ sample 3; Danio rerio; RNA Seq", "GSM3396887", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396887", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_03_14120_TAGCTT_L001_R1_001.fastq.gz", "fastq", 407925846.0, 7998546.0, "GSM3396887 r1", "0:51", "A:95664418;C:101106745;G:99163612;T:111801493;N:189578", 51, null, null, null, 95664418, 101106745, 99163612, 111801493, 189578, "SRX4721387", "SRS3806475", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95163, null, 0.03911, null, 0.80308, null, 0.47176, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49291, "SRR7883080", "SRX4721387", "SRS3806475", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 3", "GSM3396887", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396887", "GSM3396887: Wild type resting REST++ sample 3; Danio rerio; RNA Seq", "GSM3396887", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396887", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_03_14120_TAGCTT_L002_R1_001.fastq.gz", "fastq", 403131897.0, 7904547.0, "GSM3396887 r2", "0:51", "A:94571267;C:99984137;G:98039941;T:110500771;N:35781", 51, null, null, null, 94571267, 99984137, 98039941, 110500771, 35781, "SRX4721387", "SRS3806475", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95153, null, 0.03927, null, 0.80081, null, 0.43253, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49292, "SRR7883077", "SRX4721386", "SRS3806474", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 2", "GSM3396886", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396886", "GSM3396886: Wild type resting REST++ sample 2; Danio rerio; RNA Seq", "GSM3396886", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396886", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_02_14119_GATCAG_L001_R1_001.fastq.gz", "fastq", 321180252.0, 6297652.0, "GSM3396886 r1", "0:51", "A:76187242;C:79646315;G:76288340;T:88907254;N:151101", 51, null, null, null, 76187242, 79646315, 76288340, 88907254, 151101, "SRX4721386", "SRS3806474", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95633, null, 0.0376, null, 0.82294, null, 0.48192, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49293, "SRR7883078", "SRX4721386", "SRS3806474", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 2", "GSM3396886", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396886", "GSM3396886: Wild type resting REST++ sample 2; Danio rerio; RNA Seq", "GSM3396886", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396886", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_02_14119_GATCAG_L002_R1_001.fastq.gz", "fastq", 318001371.0, 6235321.0, "GSM3396886 r2", "0:51", "A:75443385;C:78910190;G:75585800;T:88033421;N:28575", 51, null, null, null, 75443385, 78910190, 75585800, 88033421, 28575, "SRX4721386", "SRS3806474", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95684, null, 0.03736, null, 0.8228, null, 0.42199, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49294, "SRR7883075", "SRX4721385", "SRS3806473", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 1", "GSM3396885", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396885", "GSM3396885: Wild type resting REST++ sample 1; Danio rerio; RNA Seq", "GSM3396885", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396885", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_01_14118_ACTTGA_L001_R1_001.fastq.gz", "fastq", 332939526.0, 6528226.0, "GSM3396885 r1", "0:51", "A:79370894;C:82057170;G:79743998;T:91615147;N:152317", 51, null, null, null, 79370894, 82057170, 79743998, 91615147, 152317, "SRX4721385", "SRS3806473", "SRA780034", "GEO", "ZF-screens BV", 1, 0.9559, null, 0.03764, null, 0.81146, null, 0.48877, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49295, "SRR7883076", "SRX4721385", "SRS3806473", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth and showed that exercised zebrafish which indeed showed enhanced growth had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds with highest growth at optimal speeds. In the Gr mutant fish exercise resulted in growth enhancement similar to wild type zebrafish indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3 Gr mutant resting REST ; n=3 wild type swimming UOPT++; n=3 Gr mutant swimming UOPT ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 1", "GSM3396885", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al. 2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al. 2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber 2014 Differentially expressed genes were identified using DESeq Anders and Huber 2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt UOPT versus REST DiffExpr.txt REST versus REST++ DiffExpr.txt and UOPT versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina San Diego CA USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396885", "GSM3396885: Wild type resting REST++ sample 1; Danio rerio; RNA Seq", "GSM3396885", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at 20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV Venlo the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific Amsterdam the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent Amstelveen Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.", "GEO Accession:GSM3396885", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_01_14118_ACTTGA_L002_R1_001.fastq.gz", "fastq", 328832853.0, 6447703.0, "GSM3396885 r2", "0:51", "A:78396828;C:81102360;G:78796819;T:90507746;N:29100", 51, null, null, null, 78396828, 81102360, 78796819, 90507746, 29100, "SRX4721385", "SRS3806473", "SRA780034", "GEO", "ZF-screens BV", 1, 0.9556, null, 0.03749, null, 0.81144, null, 0.48578, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [52173, "SRR10902874", "SRX7571044", "SRS6006645", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.", null, "pubmed:34660600", null, "muscle 2", "GSM4274620", null, "source name:muscle|strain:Tubingen|tissue:muscle|genotype:wild type", "muscle 2", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.", "muscle", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:muscle|genotype:wild type", "GSM4274620", "GSM4274620: muscle 2; Danio rerio; RNA Seq", "GSM4274620", null, "1", "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM4274620", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:GRCz10|intentional duplicate", "muscle2.bam", "bam", 16930081042.0, 56059871.0, "GSM4274620 r1", "0:151 1:151", "A:4603243415;C:3058165767;G:2976076252;T:6287916322;N:4679286", 151, 151, null, null, 4603243415, 3058165767, 2976076252, 6287916322, 4679286, "SRX7571044", "SRS6006645", "SRA880843", "GEO", "Zhejiang University", 2, 3e-05, 0.62236, 0.0, 0.0478, 0.99997, 0.86547, 1.0, 0.64653, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2020-01-16", "Undetermined", "Multi-stage", "Muscle", "Muscular System"], [52174, "SRR10902873", "SRX7571043", "SRS6006644", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.", null, "pubmed:34660600", null, "muscle 1", "GSM4274619", null, "source name:muscle|strain:Tubingen|tissue:muscle|genotype:wild type", "muscle 1", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.", "muscle", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:muscle|genotype:wild type", "GSM4274619", "GSM4274619: muscle 1; Danio rerio; RNA Seq", "GSM4274619", null, "1", "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM4274619", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:GRCz10|intentional duplicate", "muscle1.bam", "bam", 16720405462.0, 55365581.0, "GSM4274619 r1", "0:151 1:151", "A:4156663457;C:3083564895;G:3052902778;T:6423378000;N:3896332", 151, 151, null, null, 4156663457, 3083564895, 3052902778, 6423378000, 3896332, "SRX7571043", "SRS6006644", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.65433, 0.0, 0.02201, 1.0, 0.88237, null, 0.6721, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2020-01-16", "Undetermined", "Multi-stage", "Muscle", "Muscular System"], [52184, "SRR9058963", "SRX5835163", "SRS4761459", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.", null, "pubmed:34660600", null, "Muscle2", "GSM3768160", null, "source name:muscle|strain:Tubingen|genotype/variation:wild type|tissue:muscle", "Muscle2", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.", "muscle", null, "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype/variation:wild type|tissue:muscle", "GSM3768160", "GSM3768160: Muscle2; Danio rerio; RNA Seq", "GSM3768160", null, "1", "Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3768160", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index", "Muscle2.bam", "bam", 23974175100.0, 79913917.0, "GSM3768160 r1", "0:150 1:150", "A:5944663891;C:3921811959;G:4069898582;T:10035651088;N:2149580", 150, 150, null, null, 5944663891, 3921811959, 4069898582, 10035651088, 2149580, "SRX5835163", "SRS4761459", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.73445, 0.0, 0.02498, 1.0, 0.85267, null, 0.59746, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-05-15", "Undetermined", "Multi-stage", "Muscle", "Muscular System"], [56291, "SRR10903545", "SRX7571714", "SRS6007290", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 3", "GSM4274800", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 3", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274800", "GSM4274800: Zebrafish DMSO Rep 3; Danio rerio; RNA Seq", "GSM4274800", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274800", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z3_S3_R2_001.fastq.gz DMSO-Z3_S3_R1_001.fastq.gz", "fastq fastq", 3131766552.0, 41732800.0, "GSM4274800 r1", "0:37.52 1:37.52", "A:885347014;C:656593900;G:658966405;T:930204699;N:654534", 37, 37, null, null, 885347014, 656593900, 658966405, 930204699, 654534, "SRX7571714", "SRS6007290", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.9017, 0.90284, 0.20295, 0.20352, 0.726, 0.72681, 0.4835, 0.48166, 37, 36, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56292, "SRR10903544", "SRX7571713", "SRS6007289", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 2", "GSM4274799", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 2", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274799", "GSM4274799: Zebrafish DMSO Rep 2; Danio rerio; RNA Seq", "GSM4274799", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274799", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z2_S2_R2_001.fastq.gz DMSO-Z2_S2_R1_001.fastq.gz", "fastq fastq", 3602763184.0, 48016122.0, "GSM4274799 r1", "0:37.52 1:37.52", "A:1036072046;C:737502030;G:741972436;T:1086457828;N:758844", 37, 37, null, null, 1036072046, 737502030, 741972436, 1086457828, 758844, "SRX7571713", "SRS6007289", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89788, 0.8998, 0.22198, 0.22328, 0.72324, 0.72612, 0.47822, 0.47673, 38, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56293, "SRR10903543", "SRX7571712", "SRS6007288", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish DMSO Rep 1", "GSM4274798", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:DMSO", "Zebrafish DMSO Rep 1", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:DMSO", "GSM4274798", "GSM4274798: Zebrafish DMSO Rep 1; Danio rerio; RNA Seq", "GSM4274798", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "DMSO-Z1_S1_R2_001.fastq.gz DMSO-Z1_S1_R1_001.fastq.gz", "fastq fastq", 3604342960.0, 48032922.0, "GSM4274798 r1", "0:37.52 1:37.52", "A:1012371470;C:761879249;G:766369377;T:1062980320;N:742544", 37, 37, null, null, 1012371470, 761879249, 766369377, 1062980320, 742544, "SRX7571712", "SRS6007288", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90147, 0.90411, 0.18135, 0.18178, 0.72756, 0.72989, 0.48286, 0.484, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56294, "SRR10903542", "SRX7571711", "SRS6007287", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 3", "GSM4274797", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 3", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274797", "GSM4274797: Zebrafish NFA Rep 3; Danio rerio; RNA Seq", "GSM4274797", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274797", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z3_S9_R2_001.fastq.gz NFA-Z3_S9_R1_001.fastq.gz", "fastq fastq", 2585502086.0, 34448695.0, "GSM4274797 r1", "0:37.53 1:37.53", "A:703025617;C:569504763;G:571097453;T:741333725;N:540528", 37, 37, null, null, 703025617, 569504763, 571097453, 741333725, 540528, "SRX7571711", "SRS6007287", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90534, 0.90734, 0.17389, 0.17443, 0.72569, 0.72689, 0.47635, 0.47915, 36, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56295, "SRR10903541", "SRX7571710", "SRS6007286", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 2", "GSM4274796", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 2", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274796", "GSM4274796: Zebrafish NFA Rep 2; Danio rerio; RNA Seq", "GSM4274796", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z2_S8_R2_001.fastq.gz NFA-Z2_S8_R1_001.fastq.gz", "fastq fastq", 3166928712.0, 42208361.0, "GSM4274796 r1", "0:37.52 1:37.52", "A:922958966;C:638285887;G:640244924;T:964802852;N:636083", 37, 37, null, null, 922958966, 638285887, 640244924, 964802852, 636083, "SRX7571710", "SRS6007286", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.8974, 0.89826, 0.21803, 0.21778, 0.72679, 0.72825, 0.48119, 0.48197, 37, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56296, "SRR10903540", "SRX7571709", "SRS6007285", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish NFA Rep 1", "GSM4274795", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:NFA", "Zebrafish NFA Rep 1", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:NFA", "GSM4274795", "GSM4274795: Zebrafish NFA Rep 1; Danio rerio; RNA Seq", "GSM4274795", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "NFA-Z1_S7_R2_001.fastq.gz NFA-Z1_S7_R1_001.fastq.gz", "fastq fastq", 2962555966.0, 39481568.0, "GSM4274795 r1", "0:37.52 1:37.52", "A:850455036;C:607610800;G:611012952;T:892860213;N:616965", 37, 37, null, null, 850455036, 607610800, 611012952, 892860213, 616965, "SRX7571709", "SRS6007285", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89392, 0.89571, 0.25628, 0.25686, 0.72153, 0.72297, 0.47614, 0.47823, 38, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56297, "SRR10903539", "SRX7571708", "SRS6007284", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 3", "GSM4274794", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 3", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274794", "GSM4274794: Zebrafish LPA Rep 3; Danio rerio; RNA Seq", "GSM4274794", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274794", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "LPA-Z3_S6_R2_001.fastq.gz LPA-Z3_S6_R1_001.fastq.gz", "fastq fastq", 3066652967.0, 40865355.0, "GSM4274794 r1", "0:37.52 1:37.52", "A:864150135;C:645040202;G:648074884;T:908748285;N:639461", 37, 37, null, null, 864150135, 645040202, 648074884, 908748285, 639461, "SRX7571708", "SRS6007284", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89879, 0.89988, 0.21861, 0.21824, 0.72705, 0.72953, 0.47984, 0.48124, 36, 37, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56298, "SRR10903538", "SRX7571707", "SRS6007283", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 2", "GSM4274793", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 2", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274793", "GSM4274793: Zebrafish LPA Rep 2; Danio rerio; RNA Seq", "GSM4274793", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274793", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "LPA-Z2_S5_R2_001.fastq.gz LPA-Z2_S5_R1_001.fastq.gz", "fastq fastq", 3259713731.0, 43430992.0, "GSM4274793 r1", "0:37.53 1:37.53", "A:889586274;C:714766857;G:716243885;T:938441843;N:674872", 37, 37, null, null, 889586274, 714766857, 716243885, 938441843, 674872, "SRX7571707", "SRS6007283", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.90057, 0.90315, 0.2034, 0.20364, 0.72583, 0.72819, 0.48128, 0.48201, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [56299, "SRR10903537", "SRX7571706", "SRS6007282", "SRP242229", "PRJNA601746", "Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species", "GSE143801", "Other", "Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.", null, null, null, "Zebrafish LPA Rep 1", "GSM4274792", null, "tissue:zebrafish myogenic progenitor cells|cell type:myogenic progenitor cells|treatment:LPA", "Zebrafish LPA Rep 1", "Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM", "zebrafish myogenic progenitor cells", "Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37\u00b0C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz\u2019s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham\u2019s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28\u00b0C without xxx for 48 hours.", "cell type:myogenic progenitor cells|treatment:LPA", "GSM4274792", "GSM4274792: Zebrafish LPA Rep 1; Danio rerio; RNA Seq", "GSM4274792", null, "1", "Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.", "GEO Accession:GSM4274792", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP242229", null, null, "LPA-Z1_S4_R2_001.fastq.gz LPA-Z1_S4_R1_001.fastq.gz", "fastq fastq", 2616479059.0, 34861517.0, "GSM4274792 r1", "0:37.53 1:37.53", "A:703413035;C:586630572;G:585887430;T:740028263;N:519759", 37, 37, null, null, 703413035, 586630572, 585887430, 740028263, 519759, "SRX7571706", "SRS6007282", "SRA1027312", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.9153, 0.91479, 0.15809, 0.1583, 0.72936, 0.73064, 0.48034, 0.46478, 38, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-01-16", "Undetermined", "Embryo", "Muscle", "Muscular System"], [63901, "SRR14213392", "SRX10579910", "SRS8684378", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Muscle3", "GSM5237134", null, "source name:zebrafish muscle|genotype:wild type|tissue:muscle|strain:TLAB", "Muscle3", "Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish muscle", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:muscle|strain:TLAB", "GSM5237134", "GSM5237134: Muscle3; Danio rerio; RNA Seq", "GSM5237134", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237134", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Muscle3.fastq", "fastq", 1248063700.0, 12480637.0, "GSM5237134 r1", "0:100", "A:316318738;C:303727991;G:295436036;T:332533144;N:47791", 100, null, null, null, 316318738, 303727991, 295436036, 332533144, 47791, "SRX10579910", "SRS8684378", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94648, null, 0.0938, null, 0.73474, null, 0.51744, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [63902, "SRR14213391", "SRX10579909", "SRS8684377", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Muscle2", "GSM5237133", null, "source name:zebrafish muscle|genotype:wild type|tissue:muscle|strain:TLAB", "Muscle2", "Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish muscle", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:muscle|strain:TLAB", "GSM5237133", "GSM5237133: Muscle2; Danio rerio; RNA Seq", "GSM5237133", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237133", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Muscle2.fastq", "fastq", 823487500.0, 8234875.0, "GSM5237133 r1", "0:100", "A:204892783;C:204949522;G:196850367;T:216763445;N:31383", 100, null, null, null, 204892783, 204949522, 196850367, 216763445, 31383, "SRX10579909", "SRS8684377", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95133, null, 0.08777, null, 0.73081, null, 0.52808, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [63903, "SRR14213390", "SRX10579908", "SRS8684376", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Muscle1", "GSM5237132", null, "source name:zebrafish muscle|genotype:wild type|tissue:muscle|strain:TLAB", "Muscle1", "Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish muscle", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:muscle|strain:TLAB", "GSM5237132", "GSM5237132: Muscle1; Danio rerio; RNA Seq", "GSM5237132", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237132", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Muscle1.fastq", "fastq", 1561939300.0, 15619393.0, "GSM5237132 r1", "0:100", "A:390941013;C:387779384;G:377636588;T:405523724;N:58591", 100, null, null, null, 390941013, 387779384, 377636588, 405523724, 58591, "SRX10579908", "SRS8684376", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95362, null, 0.08324, null, 0.7483, null, 0.49389, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [70269, "SRR19641871", "SRX15691883", "SRS13388284", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D952 muscle", "GSM6239391", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D952 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239391", "GSM6239391: Dr D952 muscle; Danio rerio; RNA Seq", "GSM6239391 r1", "GSM6239391", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D952_Muscle.R1.fastq.gz D952_Muscle.R2.fastq.gz", "fastq fastq", 14034016416.0, 92998913.0, "GSM6239391 r1", "0:75.51 1:75.40", "A:3626008907;C:3276288577;G:3379704474;T:3741159007;N:10855451", 75, 75, null, null, 3626008907, 3276288577, 3379704474, 3741159007, 10855451, "SRX15691883", "SRS13388284", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.97042, 0.97347, 0.07223, 0.04214, 0.82538, 0.82927, 0.55476, 0.56579, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70270, "SRR19641872", "SRX15691882", "SRS13388283", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D951 muscle", "GSM6239390", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D951 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239390", "GSM6239390: Dr D951 muscle; Danio rerio; RNA Seq", "GSM6239390 r1", "GSM6239390", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D951_Muscle.R1.fastq.gz D951_Muscle.R2.fastq.gz", "fastq fastq", 11587035969.0, 76778498.0, "GSM6239390 r1", "0:75.50 1:75.42", "A:3071420513;C:2643075340;G:2733408804;T:3130418227;N:8713085", 75, 75, null, null, 3071420513, 2643075340, 2733408804, 3130418227, 8713085, "SRX15691882", "SRS13388283", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.96746, 0.96774, 0.10063, 0.06529, 0.74819, 0.75444, 0.55536, 0.56065, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70271, "SRR19641879", "SRX15691881", "SRS13388282", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D950 muscle", "GSM6239389", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D950 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239389", "GSM6239389: Dr D950 muscle; Danio rerio; RNA Seq", "GSM6239389 r1", "GSM6239389", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D950_Muscle.R1.fastq.gz D950_Muscle.R2.fastq.gz", "fastq fastq", 10339671472.0, 68539957.0, "GSM6239389 r1", "0:75.42 1:75.44", "A:2767403244;C:2295939873;G:2397017404;T:2865891007;N:13419944", 75, 75, null, null, 2767403244, 2295939873, 2397017404, 2865891007, 13419944, "SRX15691881", "SRS13388282", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.97131, 0.97203, 0.0769, 0.04197, 0.82215, 0.82554, 0.61202, 0.621, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70272, "SRR19641873", "SRX15691880", "SRS13388281", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D949 muscle", "GSM6239388", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D949 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239388", "GSM6239388: Dr D949 muscle; Danio rerio; RNA Seq", "GSM6239388 r1", "GSM6239388", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D949_Muscle.R1.fastq.gz D949_Muscle.R2.fastq.gz", "fastq fastq", 12062256543.0, 79950635.0, "GSM6239388 r1", "0:75.49 1:75.39", "A:3176604450;C:2731949532;G:2854109626;T:3290212961;N:9379974", 75, 75, null, null, 3176604450, 2731949532, 2854109626, 3290212961, 9379974, "SRX15691880", "SRS13388281", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.96846, 0.97192, 0.07324, 0.04176, 0.81412, 0.81793, 0.57983, 0.58149, 74, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70273, "SRR19641874", "SRX15691879", "SRS13388280", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr D948 muscle", "GSM6239387", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "Dr D948 muscle", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:118 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239387", "GSM6239387: Dr D948 muscle; Danio rerio; RNA Seq", "GSM6239387 r1", "GSM6239387", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP379972", null, "loader:fastq load.py", "D948_Muscle.R1.fastq.gz D948_Muscle.R2.fastq.gz", "fastq fastq", 13011602118.0, 86234782.0, "GSM6239387 r1", "0:75.47 1:75.41", "A:3544034201;C:2872687750;G:2988731712;T:3601227605;N:4920850", 75, 75, null, null, 3544034201, 2872687750, 2988731712, 3601227605, 4920850, "SRX15691879", "SRS13388280", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.96775, 0.97203, 0.07435, 0.04278, 0.81913, 0.83132, 0.55972, 0.63188, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70274, "SRR19641875", "SRX15691878", "SRS13388279", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr Muscle3", "GSM6239386", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:258 days|transgene:n1|cell line:n1|model:no transgene", "Dr Muscle3", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:258 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239386", "GSM6239386: Dr Muscle3; Danio rerio; RNA Seq", "GSM6239386 r1", "GSM6239386", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP379972", null, null, "A374-A375T24.R1.fastq.gz A374-A375T24.R2.fastq.gz", "fastq fastq", 2203662672.0, 21604536.0, "GSM6239386 r1", "0:51 1:51", "A:564768913;C:546327011;G:532582494;T:559523522;N:460732", 51, 51, null, null, 564768913, 546327011, 532582494, 559523522, 460732, "SRX15691878", "SRS13388279", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.83261, 0.82686, 0.07473, 0.06901, 0.80493, 0.80657, 0.49306, 0.49193, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [70275, "SRR19641876", "SRX15691877", "SRS13388278", "SRP379972", "PRJNA848822", "VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis", "GSE206039", "Other", "Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.", null, "pubmed:36656711", null, "Dr Muscle2", "GSM6239385", null, "source name:Normal Back Skeletal Muscle|tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:258 days|transgene:n1|cell line:n1|model:no transgene", "Dr Muscle2", "Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts", "Normal Back Skeletal Muscle", null, "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", "Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.", "tissue:Normal Back Skeletal Muscle|genotype:Wildtype AB/TL|age at sac:258 days|transgene:n1|cell line:n1|model:no transgene", "GSM6239385", "GSM6239385: Dr Muscle2; Danio rerio; RNA Seq", "GSM6239385 r1", "GSM6239385", "1", "For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP379972", null, null, "A374-A375T23.R1.fastq.gz A374-A375T23.R2.fastq.gz", "fastq fastq", 2450088960.0, 24020480.0, "GSM6239385 r1", "0:51 1:51", "A:646598229;C:592770801;G:584212215;T:625999341;N:508374", 51, 51, null, null, 646598229, 592770801, 584212215, 625999341, 508374, "SRX15691877", "SRS13388278", null, null, "Kendall Lab, Nationwide Children's Hospital / The Ohio State University", 2, 0.9278, 0.92032, 0.09971, 0.09347, 0.80986, 0.81028, 0.51973, 0.52123, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-06-13", "Undetermined", "Embryo", "Muscle", "Muscular System"], [72661, "SRR23048170", "SRX19001706", "SRS16421813", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "18 M4 24 NoRad", "GSM6927792", null, "source name:Muscle|tissue:Muscle|condition:Torpor|geo loc name:missing|collection date:missing", "18 M4 24 NoRad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Torpor|radiation cgy:0|temperature c:18.5|melatonin um:24", "GSM6927792", "GSM6927792: 18 M4 24 NoRad; Danio rerio; RNA Seq", "GSM6927792 r1", "GSM6927792", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_0012_S12_L001_R1_001.fastq.gz PN0320_0012_S12_L001_R2_001.fastq.gz", "fastq fastq", 2216625964.0, 21957637.0, "GSM6927792 r1", "0:50.43 1:50.52", "A:604204769;C:495482915;G:495882249;T:620889427;N:166604", 50, 50, null, null, 604204769, 495482915, 495882249, 620889427, 166604, "SRX19001706", "SRS16421813", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.9598, 0.95793, 0.08459, 0.08863, 0.8117, 0.81318, 0.65691, 0.65676, 50, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72662, "SRR23048171", "SRX19001705", "SRS16421812", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "18 M3 24 NoRad", "GSM6927791", null, "source name:Muscle|tissue:Muscle|condition:Torpor|geo loc name:missing|collection date:missing", "18 M3 24 NoRad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Torpor|radiation cgy:0|temperature c:18.5|melatonin um:24", "GSM6927791", "GSM6927791: 18 M3 24 NoRad; Danio rerio; RNA Seq", "GSM6927791 r1", "GSM6927791", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_00011_S11_L001_R1_001.fastq.gz PN0320_00011_S11_L001_R2_001.fastq.gz", "fastq fastq", 2062918539.0, 20433414.0, "GSM6927791 r1", "0:50.44 1:50.52", "A:552665146;C:469413584;G:472562709;T:568108230;N:168870", 50, 50, null, null, 552665146, 469413584, 472562709, 568108230, 168870, "SRX19001705", "SRS16421812", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.9585, 0.95783, 0.08664, 0.09023, 0.79971, 0.80144, 0.62278, 0.61825, 50, 48, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72663, "SRR23048172", "SRX19001704", "SRS16421811", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "18 M1 24 Rad", "GSM6927790", null, "source name:Muscle|tissue:Muscle|condition:Torpor+radiation|geo loc name:missing|collection date:missing", "18 M1 24 Rad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Torpor+radiation|radiation cgy:32.64|temperature c:18.5|melatonin um:24", "GSM6927790", "GSM6927790: 18 M1 24 Rad; Danio rerio; RNA Seq", "GSM6927790 r1", "GSM6927790", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_0010_S10_L001_R1_001.fastq.gz PN0320_0010_S10_L001_R2_001.fastq.gz", "fastq fastq", 2260102047.0, 22386719.0, "GSM6927790 r1", "0:50.44 1:50.52", "A:604400943;C:515255815;G:521377200;T:618920421;N:147668", 50, 50, null, null, 604400943, 515255815, 521377200, 618920421, 147668, "SRX19001704", "SRS16421811", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.96368, 0.96034, 0.07366, 0.07721, 0.81834, 0.82144, 0.63399, 0.63531, 49, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72664, "SRR23048173", "SRX19001703", "SRS16421810", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "18 F1 24 Rad", "GSM6927789", null, "source name:Muscle|tissue:Muscle|condition:Torpor+radiation|geo loc name:missing|collection date:missing", "18 F1 24 Rad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Torpor+radiation|radiation cgy:32.64|temperature c:18.5|melatonin um:24", "GSM6927789", "GSM6927789: 18 F1 24 Rad; Danio rerio; RNA Seq", "GSM6927789 r1", "GSM6927789", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_0009_S9_L001_R1_001.fastq.gz PN0320_0009_S9_L001_R2_001.fastq.gz", "fastq fastq", 2137718215.0, 21176234.0, "GSM6927789 r1", "0:50.44 1:50.51", "A:589518415;C:468034248;G:471805595;T:608202476;N:157481", 50, 50, null, null, 589518415, 468034248, 471805595, 608202476, 157481, "SRX19001703", "SRS16421810", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.95902, 0.95561, 0.08555, 0.08962, 0.81073, 0.81363, 0.64855, 0.66154, 51, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72665, "SRR23048174", "SRX19001702", "SRS16421809", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "18 M2 24 Rad", "GSM6927788", null, "source name:Muscle|tissue:Muscle|condition:Torpor+radiation|geo loc name:missing|collection date:missing", "18 M2 24 Rad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Torpor+radiation|radiation cgy:32.64|temperature c:18.5|melatonin um:24", "GSM6927788", "GSM6927788: 18 M2 24 Rad; Danio rerio; RNA Seq", "GSM6927788 r1", "GSM6927788", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_008_S8_L001_R1_001.fastq.gz PN0320_008_S8_L001_R2_001.fastq.gz", "fastq fastq", 2030494635.0, 20112784.0, "GSM6927788 r1", "0:50.44 1:50.51", "A:537958829;C:467846795;G:473301503;T:551248281;N:139227", 50, 50, null, null, 537958829, 467846795, 473301503, 551248281, 139227, "SRX19001702", "SRS16421809", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.96799, 0.96544, 0.05168, 0.05576, 0.82617, 0.82739, 0.60829, 0.60078, 51, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72666, "SRR23048175", "SRX19001701", "SRS16421808", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "28.5 F3 Ctrl NoRad", "GSM6927787", null, "source name:Muscle|tissue:Muscle|condition:Control|geo loc name:missing|collection date:missing", "28.5 F3 Ctrl NoRad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Control|radiation cgy:0|temperature c:28.5|melatonin um:0", "GSM6927787", "GSM6927787: 28.5 F3 Ctrl NoRad; Danio rerio; RNA Seq", "GSM6927787 r1", "GSM6927787", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_0006_S6_L001_R1_001.fastq.gz PN0320_0006_S6_L001_R2_001.fastq.gz", "fastq fastq", 1800412241.0, 17839207.0, "GSM6927787 r1", "0:50.41 1:50.51", "A:462759635;C:430537770;G:433332403;T:473582116;N:200317", 50, 50, null, null, 462759635, 430537770, 433332403, 473582116, 200317, "SRX19001701", "SRS16421808", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.97029, 0.96749, 0.06652, 0.06984, 0.82051, 0.82274, 0.59697, 0.59781, 51, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72667, "SRR23048176", "SRX19001700", "SRS16421807", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "28.5 F7 Ctrl NoRad", "GSM6927786", null, "source name:Muscle|tissue:Muscle|condition:Control|geo loc name:missing|collection date:missing", "28.5 F7 Ctrl NoRad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Control|radiation cgy:0|temperature c:28.5|melatonin um:0", "GSM6927786", "GSM6927786: 28.5 F7 Ctrl NoRad; Danio rerio; RNA Seq", "GSM6927786 r1", "GSM6927786", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_0005_S5_L001_R1_001.fastq.gz PN0320_0005_S5_L001_R2_001.fastq.gz", "fastq fastq", 2139428158.0, 21192983.0, "GSM6927786 r1", "0:50.43 1:50.52", "A:553052484;C:508236266;G:511711831;T:566255672;N:171905", 50, 50, null, null, 553052484, 508236266, 511711831, 566255672, 171905, "SRX19001700", "SRS16421807", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.96864, 0.96586, 0.05444, 0.05784, 0.82589, 0.82824, 0.59491, 0.5971, 51, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72668, "SRR23048177", "SRX19001699", "SRS16421806", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "28.5 F1 Ctrl Rad", "GSM6927785", null, "source name:Muscle|tissue:Muscle|condition:Radiation|geo loc name:missing|collection date:missing", "28.5 F1 Ctrl Rad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Radiation|radiation cgy:32.64|temperature c:28.5|melatonin um:0", "GSM6927785", "GSM6927785: 28.5 F1 Ctrl Rad; Danio rerio; RNA Seq", "GSM6927785 r1", "GSM6927785", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_0003_S3_L001_R1_001.fastq.gz PN0320_0003_S3_L001_R2_001.fastq.gz", "fastq fastq", 1891546117.0, 18735987.0, "GSM6927785 r1", "0:50.44 1:50.52", "A:502125154;C:434363680;G:438899220;T:516030974;N:127089", 50, 50, null, null, 502125154, 434363680, 438899220, 516030974, 127089, "SRX19001699", "SRS16421806", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.96654, 0.9638, 0.05566, 0.06014, 0.8239, 0.8266, 0.62793, 0.63121, 47, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72669, "SRR23048178", "SRX19001698", "SRS16421805", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "28.5 F2 Ctrl Rad", "GSM6927784", null, "source name:Muscle|tissue:Muscle|condition:Radiation|geo loc name:missing|collection date:missing", "28.5 F2 Ctrl Rad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Radiation|radiation cgy:32.64|temperature c:28.5|melatonin um:0", "GSM6927784", "GSM6927784: 28.5 F2 Ctrl Rad; Danio rerio; RNA Seq", "GSM6927784 r1", "GSM6927784", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_0002_S2_L001_R1_001.fastq.gz PN0320_0002_S2_L001_R2_001.fastq.gz", "fastq fastq", 1993571088.0, 19751994.0, "GSM6927784 r1", "0:50.42 1:50.51", "A:525369176;C:463140815;G:465749997;T:539110618;N:200482", 50, 50, null, null, 525369176, 463140815, 465749997, 539110618, 200482, "SRX19001698", "SRS16421805", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.96751, 0.96513, 0.05986, 0.06243, 0.82522, 0.82704, 0.61116, 0.61156, 50, 51, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-01-11", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [72670, "SRR23048179", "SRX19001697", "SRS16421804", "SRP416971", "PRJNA922874", "Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle", "GSE222614", "Transcriptome Analysis", "The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However mounting evidence points to torpor induced protective benefits from the main hazards of space travel namely exposure to radiation and microgravity. To determine the radio protective effects of an induced torpor like state we exploited the ectothermic nature of the Danio rerio zebrafish in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low dose radiation 0.3Gy to simulate radiation exposure on long term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition DNA repair processes were downregulated in the muscle two days' post irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex tracellular matrix and developmental genes. Upon radiation exposure increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im mune related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross species comparison was performed with the muscle of hibernating Ursus arctos horribilis brown bear to define shared mechanisms of cold tolerance. Shared responses show an upregula tion of protein translation and metabolism of amino acids as well as a hypoxia response with the shared downregulation of glycolysis ECM and developmental genes. Overall design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation", null, null, null, "28.5 F7 Ctrl Rad", "GSM6927783", null, "source name:Muscle|tissue:Muscle|condition:Radiation|geo loc name:missing|collection date:missing", "28.5 F7 Ctrl Rad", "Sequence quality was assessed with FastQC to identify over represented sequences and low quality reads Low quality reads and over represented sequences were removed with Cutadapt The STAR aligner was utilised to align the RNA Seq reads to the zebrafish genome GRCz11 HTSeq was used to determine the number of reads per transcript DESeq2 was used for determination of differentially expressed genes Assembly: zebrafish genome GRCz11", "Muscle", "A melatonin group 28.5 melatonin received melatonin daily for 10 days at a concentration of 24 \u00b5M for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10\u00b0C from 28.5\u00b0C to 18.5\u00b0C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10\u00b0C reduction in ambient temperature and the addition of 24 \u00b5M melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen\u2019s miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer\u2019s protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "tissue:Muscle|condition:Radiation|radiation cgy:32.64|temperature c:28.5|melatonin um:0", "GSM6927783", "GSM6927783: 28.5 F7 Ctrl Rad; Danio rerio; RNA Seq", "GSM6927783 r1", "GSM6927783", "1", "Total mRNA was extracted from liver tissue of the zebrafish using Qiagen's miRNeasy Mini kit Qiagen Hilden Germany. To prepare mRNA seq kit poly A capture KAPA RNA hyperIllumina San Diego CA USA; was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer's protocol. High through put RNA sequencing RNAseq was performed at the Queens University Belfast Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded PE50 strategy.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP416971", null, "loader:fastq load.py", "PN0320_0001_S1_L001_R1_001.fastq.gz PN0320_0001_S1_L001_R2_001.fastq.gz", "fastq fastq", 2532727358.0, 25091050.0, "GSM6927783 r1", "0:50.42 1:50.52", "A:652264108;C:605047979;G:607887475;T:667327837;N:199959", 50, 50, null, null, 652264108, 605047979, 607887475, 667327837, 199959, "SRX19001697", "SRS16421804", "SRA1572773", "Queens university Belfast", "Queens university Belfast", 2, 0.97088, 0.96851, 0.05232, 0.05605, 0.83704, 0.83855, 0.51127, 0.57751, 51, 50, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", 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