{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Undetermined\" and tissue_curation_coarse = \"Muscular System\"", "rows": [[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"], [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"], [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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