metadata: run_metadata: 61 rows where devstage_curation = "Undetermined" and tissue_curation

61 rows where devstage_curation = "Undetermined" and tissue_curation_coarse = "Muscular System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
36665	36665	SRR800045	SRX257154	SRS405708	SRP020008	PRJNA193544	Danio rerio strain:Tubingen Epigenomics	PRJNA193544	Other	Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.	pubmed:23663776	Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.	Generic sample from Danio rerio	muscle RNAseq totalRNARibominus	strain:Tubingen\|label:PE: paired end SE: single end\|development stage:muscle									muscle RNAseq totalRNARibominus	muscle RNAseq totalRNARibominus	9084X1	Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 1000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP020008		muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz	Illumina native	3506573750.0	70131475.0	9084X1 120420 SN141 0500 AD0TG5ACXX 5	0:50	A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806	50		872717534	808774955	1036781008	777391447	10908806	SRX257154	SRS405708	SRA072148	University of Utah\|Brad Cairns Lab	University of Utah	1	0.61428		0.09813		0.89305		0.6908		50		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	unknown	bulk	unknown	unknown	United States	2013-05-07	Undetermined	Embryo	Muscle	Muscular System
49268	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.	pubmed:30692930		Gr mutant swimming UOPT sample 3	GSM3396896	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:swimming\|tissue:white muscle	GSM3396896	GSM3396896: Gr mutant swimming UOPT sample 3; Danio rerio; RNA Seq	GSM3396896		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 ºC. 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 μl 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 μg 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		SRP162257		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		56574599	63639902	59333109	68728919	135036	SRX4721396	SRS3806484	SRA780034	GEO	ZF-screens BV	1	0.95963		0.03133		0.82144		0.50958		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49269	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.	pubmed:30692930		Gr mutant swimming UOPT sample 3	GSM3396896	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:swimming\|tissue:white muscle	GSM3396896	GSM3396896: Gr mutant swimming UOPT sample 3; Danio rerio; RNA Seq	GSM3396896		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 ºC. 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 μl 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 μg 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		SRP162257		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		55999278	63022234	58753181	68048742	45066	SRX4721396	SRS3806484	SRA780034	GEO	ZF-screens BV	1	0.9607		0.03061		0.81876		0.50656		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49270	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.	pubmed:30692930		Gr mutant swimming UOPT sample 2	GSM3396895	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:swimming\|tissue:white muscle	GSM3396895	GSM3396895: Gr mutant swimming UOPT sample 2; Danio rerio; RNA Seq	GSM3396895		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 ºC. 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 μl 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 μg 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		SRP162257		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		48361086	57271498	53468696	60291615	121101	SRX4721395	SRS3806483	SRA780034	GEO	ZF-screens BV	1	0.95734		0.02232		0.83037		0.46039		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49271	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.	pubmed:30692930		Gr mutant swimming UOPT sample 2	GSM3396895	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:swimming\|tissue:white muscle	GSM3396895	GSM3396895: Gr mutant swimming UOPT sample 2; Danio rerio; RNA Seq	GSM3396895		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 ºC. 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 μl 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 μg 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		SRP162257		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		47895589	56699017	52953041	59691639	39890	SRX4721395	SRS3806483	SRA780034	GEO	ZF-screens BV	1	0.95882		0.02375		0.82753		0.45523		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49272	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.	pubmed:30692930		Gr mutant swimming UOPT sample 1	GSM3396894	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:swimming\|tissue:white muscle	GSM3396894	GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq	GSM3396894		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 ºC. 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 μl 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 μg 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		SRP162257		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		17764968	19359482	17546237	21458644	13516	SRX4721394	SRS3806482	SRA780034	GEO	ZF-screens BV	1	0.94854		0.03967		0.81239		0.52843		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49273	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.	pubmed:30692930		Gr mutant swimming UOPT sample 1	GSM3396894	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:swimming\|tissue:white muscle	GSM3396894	GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq	GSM3396894		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 ºC. 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 μl 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 μg 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		SRP162257		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		17559056	19128796	17344883	21206265	6655	SRX4721394	SRS3806482	SRA780034	GEO	ZF-screens BV	1	0.95076		0.03952		0.81057		0.52805		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49274	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.	pubmed:30692930		Gr mutant swimming UOPT sample 1	GSM3396894	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:swimming\|tissue:white muscle	GSM3396894	GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq	GSM3396894		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 ºC. 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 μl 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 μg 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		SRP162257		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		65346157	71914444	66015753	79625150	40580	SRX4721394	SRS3806482	SRA780034	GEO	ZF-screens BV	1	0.95533		0.03742		0.81044		0.52574		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49275	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.	pubmed:30692930		Gr mutant swimming UOPT sample 1	GSM3396894	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:swimming\|tissue:white muscle	GSM3396894	GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq	GSM3396894		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 ºC. 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 μl 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 μg 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		SRP162257		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		64447735	70937019	65137622	78531620	47278	SRX4721394	SRS3806482	SRA780034	GEO	ZF-screens BV	1	0.95428		0.03783		0.81128		0.52701		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49276	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.	pubmed:30692930		Wild type swimming UOPT++ sample 3	GSM3396893	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:swimming\|tissue:white muscle	GSM3396893	GSM3396893: Wild type swimming UOPT++ sample 3; Danio rerio; RNA Seq	GSM3396893		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 ºC. 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 μl 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 μg 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		SRP162257		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		84489335	86597253	84240000	99472362	195016	SRX4721393	SRS3806481	SRA780034	GEO	ZF-screens BV	1	0.95532		0.04239		0.80653		0.55623		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49277	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.	pubmed:30692930		Wild type swimming UOPT++ sample 3	GSM3396893	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:swimming\|tissue:white muscle	GSM3396893	GSM3396893: Wild type swimming UOPT++ sample 3; Danio rerio; RNA Seq	GSM3396893		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 ºC. 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 μl 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 μg 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		SRP162257		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		83629618	85716733	83395630	98483376	64836	SRX4721393	SRS3806481	SRA780034	GEO	ZF-screens BV	1	0.95631		0.04199		0.8056		0.54571		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49278	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.	pubmed:30692930		Wild type swimming UOPT++ sample 2	GSM3396892	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:swimming\|tissue:white muscle	GSM3396892	GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq	GSM3396892		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 ºC. 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 μl 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 μg 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		SRP162257		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		16926874	17543094	16728407	19679197	12377	SRX4721392	SRS3806480	SRA780034	GEO	ZF-screens BV	1	0.95627		0.03548		0.82451		0.53415		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49279	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.	pubmed:30692930		Wild type swimming UOPT++ sample 2	GSM3396892	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:swimming\|tissue:white muscle	GSM3396892	GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq	GSM3396892		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 ºC. 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 μl 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 μg 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		SRP162257		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		16757913	17378481	16577230	19498501	6001	SRX4721392	SRS3806480	SRA780034	GEO	ZF-screens BV	1	0.95571		0.03554		0.82806		0.50999		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49280	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.	pubmed:30692930		Wild type swimming UOPT++ sample 2	GSM3396892	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:swimming\|tissue:white muscle	GSM3396892	GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq	GSM3396892		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 ºC. 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 μl 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 μg 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		SRP162257		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		65379164	68332333	65926683	76572534	40527	SRX4721392	SRS3806480	SRA780034	GEO	ZF-screens BV	1	0.96013		0.0352		0.82814		0.53974		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49281	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.	pubmed:30692930		Wild type swimming UOPT++ sample 2	GSM3396892	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:swimming\|tissue:white muscle	GSM3396892	GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq	GSM3396892		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 ºC. 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 μl 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 μg 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		SRP162257		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		64737712	67666247	65306231	75803211	46927	SRX4721392	SRS3806480	SRA780034	GEO	ZF-screens BV	1	0.95941		0.03355		0.82745		0.54235		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49282	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.	pubmed:30692930		Wild type swimming UOPT++ sample 1	GSM3396891	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:swimming\|tissue:white muscle	GSM3396891	GSM3396891: Wild type swimming UOPT++ sample 1; Danio rerio; RNA Seq	GSM3396891		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 ºC. 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 μl 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 μg 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		SRP162257		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		93242107	96684654	92114654	109292193	177378	SRX4721391	SRS3806479	SRA780034	GEO	ZF-screens BV	1	0.95344		0.05682		0.80612		0.46874		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49283	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.	pubmed:30692930		Wild type swimming UOPT++ sample 1	GSM3396891	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:swimming\|tissue:white muscle	GSM3396891	GSM3396891: Wild type swimming UOPT++ sample 1; Danio rerio; RNA Seq	GSM3396891		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 ºC. 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 μl 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 μg 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		SRP162257		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		92211053	95616109	91125664	108078262	34483	SRX4721391	SRS3806479	SRA780034	GEO	ZF-screens BV	1	0.95555		0.05726		0.80655		0.50316		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49284	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.	pubmed:30692930		Gr mutant resting REST sample 3	GSM3396890	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:resting\|tissue:white muscle	GSM3396890	GSM3396890: Gr mutant resting REST sample 3; Danio rerio; RNA Seq	GSM3396890		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 ºC. 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 μl 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 μg 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		SRP162257		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		93056953	102519574	95945518	110623659	188094	SRX4721390	SRS3806478	SRA780034	GEO	ZF-screens BV	1	0.96072		0.03044		0.83151		0.49904		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49285	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.	pubmed:30692930		Gr mutant resting REST sample 3	GSM3396890	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:resting\|tissue:white muscle	GSM3396890	GSM3396890: Gr mutant resting REST sample 3; Danio rerio; RNA Seq	GSM3396890		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 ºC. 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 μl 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 μg 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		SRP162257		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		92045457	101410388	94956743	109396044	35534	SRX4721390	SRS3806478	SRA780034	GEO	ZF-screens BV	1	0.96026		0.03027		0.82994		0.49932		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49286	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.	pubmed:30692930		Gr mutant resting REST sample 2	GSM3396889	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:resting\|tissue:white muscle	GSM3396889	GSM3396889: Gr mutant resting REST sample 2; Danio rerio; RNA Seq	GSM3396889		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 ºC. 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 μl 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 μg 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		SRP162257		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		96524820	105111599	96647633	116788874	192381	SRX4721389	SRS3806477	SRA780034	GEO	ZF-screens BV	1	0.95102		0.04156		0.79164		0.52657		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49287	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.	pubmed:30692930		Gr mutant resting REST sample 2	GSM3396889	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:resting\|tissue:white muscle	GSM3396889	GSM3396889: Gr mutant resting REST sample 2; Danio rerio; RNA Seq	GSM3396889		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 ºC. 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 μl 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 μg 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		SRP162257		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		95514290	104001536	95684811	115561454	36534	SRX4721389	SRS3806477	SRA780034	GEO	ZF-screens BV	1	0.95117		0.04146		0.79032		0.51379		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49288	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.	pubmed:30692930		Gr mutant resting REST sample 1	GSM3396888	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:resting\|tissue:white muscle	GSM3396888	GSM3396888: Gr mutant resting REST sample 1; Danio rerio; RNA Seq	GSM3396888		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 ºC. 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 μl 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 μg 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		SRP162257		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		83067213	89144746	86927052	96973321	161275	SRX4721388	SRS3806476	SRA780034	GEO	ZF-screens BV	1	0.9514		0.03636		0.78064		0.49277		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49289	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.	pubmed:30692930		Gr mutant resting REST sample 1	GSM3396888	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		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Gr mutant\|treatment:resting\|tissue:white muscle	GSM3396888	GSM3396888: Gr mutant resting REST sample 1; Danio rerio; RNA Seq	GSM3396888		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 ºC. 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 μl 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 μg 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		SRP162257		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		82429330	88444066	86279627	96242734	31285	SRX4721388	SRS3806476	SRA780034	GEO	ZF-screens BV	1	0.95127		0.03685		0.78125		0.49716		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49290	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.	pubmed:30692930		Wild type resting REST++ sample 3	GSM3396887	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:resting\|tissue:white muscle	GSM3396887	GSM3396887: Wild type resting REST++ sample 3; Danio rerio; RNA Seq	GSM3396887		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 ºC. 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 μl 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 μg 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		SRP162257		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		95664418	101106745	99163612	111801493	189578	SRX4721387	SRS3806475	SRA780034	GEO	ZF-screens BV	1	0.95163		0.03911		0.80308		0.47176		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49291	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.	pubmed:30692930		Wild type resting REST++ sample 3	GSM3396887	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:resting\|tissue:white muscle	GSM3396887	GSM3396887: Wild type resting REST++ sample 3; Danio rerio; RNA Seq	GSM3396887		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 ºC. 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 μl 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 μg 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		SRP162257		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		94571267	99984137	98039941	110500771	35781	SRX4721387	SRS3806475	SRA780034	GEO	ZF-screens BV	1	0.95153		0.03927		0.80081		0.43253		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49292	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.	pubmed:30692930		Wild type resting REST++ sample 2	GSM3396886	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:resting\|tissue:white muscle	GSM3396886	GSM3396886: Wild type resting REST++ sample 2; Danio rerio; RNA Seq	GSM3396886		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 ºC. 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 μl 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 μg 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		SRP162257		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		76187242	79646315	76288340	88907254	151101	SRX4721386	SRS3806474	SRA780034	GEO	ZF-screens BV	1	0.95633		0.0376		0.82294		0.48192		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49293	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.	pubmed:30692930		Wild type resting REST++ sample 2	GSM3396886	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:resting\|tissue:white muscle	GSM3396886	GSM3396886: Wild type resting REST++ sample 2; Danio rerio; RNA Seq	GSM3396886		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 ºC. 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 μl 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 μg 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		SRP162257		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		75443385	78910190	75585800	88033421	28575	SRX4721386	SRS3806474	SRA780034	GEO	ZF-screens BV	1	0.95684		0.03736		0.8228		0.42199		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49294	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.	pubmed:30692930		Wild type resting REST++ sample 1	GSM3396885	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:resting\|tissue:white muscle	GSM3396885	GSM3396885: Wild type resting REST++ sample 1; Danio rerio; RNA Seq	GSM3396885		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 ºC. 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 μl 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 μg 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		SRP162257		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		79370894	82057170	79743998	91615147	152317	SRX4721385	SRS3806473	SRA780034	GEO	ZF-screens BV	1	0.9559		0.03764		0.81146		0.48877		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
49295	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.	pubmed:30692930		Wild type resting REST++ sample 1	GSM3396885	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++		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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.		tissue:white muscle\|genotype:Wild type\|treatment:resting\|tissue:white muscle	GSM3396885	GSM3396885: Wild type resting REST++ sample 1; Danio rerio; RNA Seq	GSM3396885		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 ºC. 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 μl 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 μg 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		SRP162257		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		78396828	81102360	78796819	90507746	29100	SRX4721385	SRS3806473	SRA780034	GEO	ZF-screens BV	1	0.9556		0.03749		0.81144		0.48578		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2018-09-20	Undetermined	Undetermined	Muscle	Muscular System
52173	52173	SRR10902874	SRX7571044	SRS6006645	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600		muscle 2	GSM4274620	source name:muscle\|strain:Tubingen\|tissue:muscle\|genotype:wild type	muscle 2	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	muscle		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|tissue:muscle\|genotype:wild type	GSM4274620	GSM4274620: muscle 2; Danio rerio; RNA Seq	GSM4274620		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM4274620	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP194254	assembly:GRCz10\|intentional duplicate	muscle2.bam	bam	16930081042.0	56059871.0	GSM4274620 r1	0:151 1:151	A:4603243415;C:3058165767;G:2976076252;T:6287916322;N:4679286	151	151	4603243415	3058165767	2976076252	6287916322	4679286	SRX7571044	SRS6006645	SRA880843	GEO	Zhejiang University	2	3e-05	0.62236	0.0	0.0478	0.99997	0.86547	1.0	0.64653	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2020-01-16	Undetermined	Multi-stage	Muscle	Muscular System
52174	52174	SRR10902873	SRX7571043	SRS6006644	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600		muscle 1	GSM4274619	source name:muscle\|strain:Tubingen\|tissue:muscle\|genotype:wild type	muscle 1	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	muscle		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|tissue:muscle\|genotype:wild type	GSM4274619	GSM4274619: muscle 1; Danio rerio; RNA Seq	GSM4274619		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM4274619	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP194254	assembly:GRCz10\|intentional duplicate	muscle1.bam	bam	16720405462.0	55365581.0	GSM4274619 r1	0:151 1:151	A:4156663457;C:3083564895;G:3052902778;T:6423378000;N:3896332	151	151	4156663457	3083564895	3052902778	6423378000	3896332	SRX7571043	SRS6006644	SRA880843	GEO	Zhejiang University	2	0.0	0.65433	0.0	0.02201	1.0	0.88237		0.6721	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2020-01-16	Undetermined	Multi-stage	Muscle	Muscular System
52184	52184	SRR9058963	SRX5835163	SRS4761459	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.	pubmed:34660600		Muscle2	GSM3768160	source name:muscle\|strain:Tubingen\|genotype/variation:wild type\|tissue:muscle	Muscle2	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	muscle		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|genotype/variation:wild type\|tissue:muscle	GSM3768160	GSM3768160: Muscle2; Danio rerio; RNA Seq	GSM3768160		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM3768160	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq X Ten		SRP194254	assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index	Muscle2.bam	bam	23974175100.0	79913917.0	GSM3768160 r1	0:150 1:150	A:5944663891;C:3921811959;G:4069898582;T:10035651088;N:2149580	150	150	5944663891	3921811959	4069898582	10035651088	2149580	SRX5835163	SRS4761459	SRA880843	GEO	Zhejiang University	2	0.0	0.73445	0.0	0.02498	1.0	0.85267		0.59746	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2019-05-15	Undetermined	Multi-stage	Muscle	Muscular System
56291	56291	SRR10903545	SRX7571714	SRS6007290	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish DMSO Rep 3	GSM4274800	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:DMSO	Zebrafish DMSO Rep 3	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:DMSO	GSM4274800	GSM4274800: Zebrafish DMSO Rep 3; Danio rerio; RNA Seq	GSM4274800		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274800	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		DMSO-Z3_S3_R2_001.fastq.gz DMSO-Z3_S3_R1_001.fastq.gz	fastq fastq	3131766552.0	41732800.0	GSM4274800 r1	0:37.52 1:37.52	A:885347014;C:656593900;G:658966405;T:930204699;N:654534	37	37	885347014	656593900	658966405	930204699	654534	SRX7571714	SRS6007290	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.9017	0.90284	0.20295	0.20352	0.726	0.72681	0.4835	0.48166	37	36	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
56292	56292	SRR10903544	SRX7571713	SRS6007289	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish DMSO Rep 2	GSM4274799	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:DMSO	Zebrafish DMSO Rep 2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:DMSO	GSM4274799	GSM4274799: Zebrafish DMSO Rep 2; Danio rerio; RNA Seq	GSM4274799		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274799	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		DMSO-Z2_S2_R2_001.fastq.gz DMSO-Z2_S2_R1_001.fastq.gz	fastq fastq	3602763184.0	48016122.0	GSM4274799 r1	0:37.52 1:37.52	A:1036072046;C:737502030;G:741972436;T:1086457828;N:758844	37	37	1036072046	737502030	741972436	1086457828	758844	SRX7571713	SRS6007289	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.89788	0.8998	0.22198	0.22328	0.72324	0.72612	0.47822	0.47673	38	37	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
56293	56293	SRR10903543	SRX7571712	SRS6007288	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish DMSO Rep 1	GSM4274798	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:DMSO	Zebrafish DMSO Rep 1	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:DMSO	GSM4274798	GSM4274798: Zebrafish DMSO Rep 1; Danio rerio; RNA Seq	GSM4274798		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274798	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		DMSO-Z1_S1_R2_001.fastq.gz DMSO-Z1_S1_R1_001.fastq.gz	fastq fastq	3604342960.0	48032922.0	GSM4274798 r1	0:37.52 1:37.52	A:1012371470;C:761879249;G:766369377;T:1062980320;N:742544	37	37	1012371470	761879249	766369377	1062980320	742544	SRX7571712	SRS6007288	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.90147	0.90411	0.18135	0.18178	0.72756	0.72989	0.48286	0.484	38	38	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
56294	56294	SRR10903542	SRX7571711	SRS6007287	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish NFA Rep 3	GSM4274797	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:NFA	Zebrafish NFA Rep 3	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:NFA	GSM4274797	GSM4274797: Zebrafish NFA Rep 3; Danio rerio; RNA Seq	GSM4274797		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274797	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		NFA-Z3_S9_R2_001.fastq.gz NFA-Z3_S9_R1_001.fastq.gz	fastq fastq	2585502086.0	34448695.0	GSM4274797 r1	0:37.53 1:37.53	A:703025617;C:569504763;G:571097453;T:741333725;N:540528	37	37	703025617	569504763	571097453	741333725	540528	SRX7571711	SRS6007287	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.90534	0.90734	0.17389	0.17443	0.72569	0.72689	0.47635	0.47915	36	38	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
56295	56295	SRR10903541	SRX7571710	SRS6007286	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish NFA Rep 2	GSM4274796	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:NFA	Zebrafish NFA Rep 2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:NFA	GSM4274796	GSM4274796: Zebrafish NFA Rep 2; Danio rerio; RNA Seq	GSM4274796		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274796	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		NFA-Z2_S8_R2_001.fastq.gz NFA-Z2_S8_R1_001.fastq.gz	fastq fastq	3166928712.0	42208361.0	GSM4274796 r1	0:37.52 1:37.52	A:922958966;C:638285887;G:640244924;T:964802852;N:636083	37	37	922958966	638285887	640244924	964802852	636083	SRX7571710	SRS6007286	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.8974	0.89826	0.21803	0.21778	0.72679	0.72825	0.48119	0.48197	37	38	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
56296	56296	SRR10903540	SRX7571709	SRS6007285	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish NFA Rep 1	GSM4274795	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:NFA	Zebrafish NFA Rep 1	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:NFA	GSM4274795	GSM4274795: Zebrafish NFA Rep 1; Danio rerio; RNA Seq	GSM4274795		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274795	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		NFA-Z1_S7_R2_001.fastq.gz NFA-Z1_S7_R1_001.fastq.gz	fastq fastq	2962555966.0	39481568.0	GSM4274795 r1	0:37.52 1:37.52	A:850455036;C:607610800;G:611012952;T:892860213;N:616965	37	37	850455036	607610800	611012952	892860213	616965	SRX7571709	SRS6007285	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.89392	0.89571	0.25628	0.25686	0.72153	0.72297	0.47614	0.47823	38	37	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
56297	56297	SRR10903539	SRX7571708	SRS6007284	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish LPA Rep 3	GSM4274794	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:LPA	Zebrafish LPA Rep 3	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:LPA	GSM4274794	GSM4274794: Zebrafish LPA Rep 3; Danio rerio; RNA Seq	GSM4274794		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274794	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		LPA-Z3_S6_R2_001.fastq.gz LPA-Z3_S6_R1_001.fastq.gz	fastq fastq	3066652967.0	40865355.0	GSM4274794 r1	0:37.52 1:37.52	A:864150135;C:645040202;G:648074884;T:908748285;N:639461	37	37	864150135	645040202	648074884	908748285	639461	SRX7571708	SRS6007284	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.89879	0.89988	0.21861	0.21824	0.72705	0.72953	0.47984	0.48124	36	37	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
56298	56298	SRR10903538	SRX7571707	SRS6007283	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish LPA Rep 2	GSM4274793	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:LPA	Zebrafish LPA Rep 2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:LPA	GSM4274793	GSM4274793: Zebrafish LPA Rep 2; Danio rerio; RNA Seq	GSM4274793		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274793	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		LPA-Z2_S5_R2_001.fastq.gz LPA-Z2_S5_R1_001.fastq.gz	fastq fastq	3259713731.0	43430992.0	GSM4274793 r1	0:37.53 1:37.53	A:889586274;C:714766857;G:716243885;T:938441843;N:674872	37	37	889586274	714766857	716243885	938441843	674872	SRX7571707	SRS6007283	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.90057	0.90315	0.2034	0.20364	0.72583	0.72819	0.48128	0.48201	38	38	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
56299	56299	SRR10903537	SRX7571706	SRS6007282	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.			Zebrafish LPA Rep 1	GSM4274792	tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:LPA	Zebrafish LPA Rep 1	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:LPA	GSM4274792	GSM4274792: Zebrafish LPA Rep 1; Danio rerio; RNA Seq	GSM4274792		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274792	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229		LPA-Z1_S4_R2_001.fastq.gz LPA-Z1_S4_R1_001.fastq.gz	fastq fastq	2616479059.0	34861517.0	GSM4274792 r1	0:37.53 1:37.53	A:703413035;C:586630572;G:585887430;T:740028263;N:519759	37	37	703413035	586630572	585887430	740028263	519759	SRX7571706	SRS6007282	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.9153	0.91479	0.15809	0.1583	0.72936	0.73064	0.48034	0.46478	38	38	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq	United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System
63901	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.	pubmed:34556579		Muscle3	GSM5237134	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		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°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:muscle\|strain:TLAB	GSM5237134	GSM5237134: Muscle3; Danio rerio; RNA Seq	GSM5237134		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		SRP314470		Muscle3.fastq	fastq	1248063700.0	12480637.0	GSM5237134 r1	0:100	A:316318738;C:303727991;G:295436036;T:332533144;N:47791	100		316318738	303727991	295436036	332533144	47791	SRX10579910	SRS8684378	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94648		0.0938		0.73474		0.51744		100		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Muscle	Muscular System
63902	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.	pubmed:34556579		Muscle2	GSM5237133	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		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°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:muscle\|strain:TLAB	GSM5237133	GSM5237133: Muscle2; Danio rerio; RNA Seq	GSM5237133		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		SRP314470		Muscle2.fastq	fastq	823487500.0	8234875.0	GSM5237133 r1	0:100	A:204892783;C:204949522;G:196850367;T:216763445;N:31383	100		204892783	204949522	196850367	216763445	31383	SRX10579909	SRS8684377	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95133		0.08777		0.73081		0.52808		100		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Muscle	Muscular System
63903	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.	pubmed:34556579		Muscle1	GSM5237132	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		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°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:muscle\|strain:TLAB	GSM5237132	GSM5237132: Muscle1; Danio rerio; RNA Seq	GSM5237132		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		SRP314470		Muscle1.fastq	fastq	1561939300.0	15619393.0	GSM5237132 r1	0:100	A:390941013;C:387779384;G:377636588;T:405523724;N:58591	100		390941013	387779384	377636588	405523724	58591	SRX10579908	SRS8684376	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95362		0.08324		0.7483		0.49389		100		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Muscle	Muscular System
70269	70269	SRR19641871	SRX15691883	SRS13388284	SRP379972	PRJNA848822	VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis	GSE206039	Other	Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.	pubmed:36656711		Dr D952 muscle	GSM6239391	source name:Normal Back Skeletal Muscle\|tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	Dr D952 muscle	Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts	Normal Back Skeletal Muscle		For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols	Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.	tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	GSM6239391	GSM6239391: Dr D952 muscle; Danio rerio; RNA Seq	GSM6239391 r1	GSM6239391	1	For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP379972	loader:fastq load.py	D952_Muscle.R1.fastq.gz D952_Muscle.R2.fastq.gz	fastq fastq	14034016416.0	92998913.0	GSM6239391 r1	0:75.51 1:75.40	A:3626008907;C:3276288577;G:3379704474;T:3741159007;N:10855451	75	75	3626008907	3276288577	3379704474	3741159007	10855451	SRX15691883	SRS13388284			Kendall Lab, Nationwide Children's Hospital / The Ohio State University	2	0.97042	0.97347	0.07223	0.04214	0.82538	0.82927	0.55476	0.56579	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-06-13	Undetermined	Embryo	Muscle	Muscular System
70270	70270	SRR19641872	SRX15691882	SRS13388283	SRP379972	PRJNA848822	VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis	GSE206039	Other	Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.	pubmed:36656711		Dr D951 muscle	GSM6239390	source name:Normal Back Skeletal Muscle\|tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	Dr D951 muscle	Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts	Normal Back Skeletal Muscle		For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols	Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.	tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	GSM6239390	GSM6239390: Dr D951 muscle; Danio rerio; RNA Seq	GSM6239390 r1	GSM6239390	1	For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP379972	loader:fastq load.py	D951_Muscle.R1.fastq.gz D951_Muscle.R2.fastq.gz	fastq fastq	11587035969.0	76778498.0	GSM6239390 r1	0:75.50 1:75.42	A:3071420513;C:2643075340;G:2733408804;T:3130418227;N:8713085	75	75	3071420513	2643075340	2733408804	3130418227	8713085	SRX15691882	SRS13388283			Kendall Lab, Nationwide Children's Hospital / The Ohio State University	2	0.96746	0.96774	0.10063	0.06529	0.74819	0.75444	0.55536	0.56065	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-06-13	Undetermined	Embryo	Muscle	Muscular System
70271	70271	SRR19641879	SRX15691881	SRS13388282	SRP379972	PRJNA848822	VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis	GSE206039	Other	Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.	pubmed:36656711		Dr D950 muscle	GSM6239389	source name:Normal Back Skeletal Muscle\|tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	Dr D950 muscle	Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts	Normal Back Skeletal Muscle		For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols	Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.	tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	GSM6239389	GSM6239389: Dr D950 muscle; Danio rerio; RNA Seq	GSM6239389 r1	GSM6239389	1	For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP379972	loader:fastq load.py	D950_Muscle.R1.fastq.gz D950_Muscle.R2.fastq.gz	fastq fastq	10339671472.0	68539957.0	GSM6239389 r1	0:75.42 1:75.44	A:2767403244;C:2295939873;G:2397017404;T:2865891007;N:13419944	75	75	2767403244	2295939873	2397017404	2865891007	13419944	SRX15691881	SRS13388282			Kendall Lab, Nationwide Children's Hospital / The Ohio State University	2	0.97131	0.97203	0.0769	0.04197	0.82215	0.82554	0.61202	0.621	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-06-13	Undetermined	Embryo	Muscle	Muscular System
70272	70272	SRR19641873	SRX15691880	SRS13388281	SRP379972	PRJNA848822	VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis	GSE206039	Other	Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.	pubmed:36656711		Dr D949 muscle	GSM6239388	source name:Normal Back Skeletal Muscle\|tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	Dr D949 muscle	Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts	Normal Back Skeletal Muscle		For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols	Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.	tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	GSM6239388	GSM6239388: Dr D949 muscle; Danio rerio; RNA Seq	GSM6239388 r1	GSM6239388	1	For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP379972	loader:fastq load.py	D949_Muscle.R1.fastq.gz D949_Muscle.R2.fastq.gz	fastq fastq	12062256543.0	79950635.0	GSM6239388 r1	0:75.49 1:75.39	A:3176604450;C:2731949532;G:2854109626;T:3290212961;N:9379974	75	75	3176604450	2731949532	2854109626	3290212961	9379974	SRX15691880	SRS13388281			Kendall Lab, Nationwide Children's Hospital / The Ohio State University	2	0.96846	0.97192	0.07324	0.04176	0.81412	0.81793	0.57983	0.58149	74	74	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-06-13	Undetermined	Embryo	Muscle	Muscular System
70273	70273	SRR19641874	SRX15691879	SRS13388280	SRP379972	PRJNA848822	VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis	GSE206039	Other	Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.	pubmed:36656711		Dr D948 muscle	GSM6239387	source name:Normal Back Skeletal Muscle\|tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	Dr D948 muscle	Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts	Normal Back Skeletal Muscle		For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols	Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.	tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:118 days\|transgene:n1\|cell line:n1\|model:no transgene	GSM6239387	GSM6239387: Dr D948 muscle; Danio rerio; RNA Seq	GSM6239387 r1	GSM6239387	1	For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP379972	loader:fastq load.py	D948_Muscle.R1.fastq.gz D948_Muscle.R2.fastq.gz	fastq fastq	13011602118.0	86234782.0	GSM6239387 r1	0:75.47 1:75.41	A:3544034201;C:2872687750;G:2988731712;T:3601227605;N:4920850	75	75	3544034201	2872687750	2988731712	3601227605	4920850	SRX15691879	SRS13388280			Kendall Lab, Nationwide Children's Hospital / The Ohio State University	2	0.96775	0.97203	0.07435	0.04278	0.81913	0.83132	0.55972	0.63188	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-06-13	Undetermined	Embryo	Muscle	Muscular System
70274	70274	SRR19641875	SRX15691878	SRS13388279	SRP379972	PRJNA848822	VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis	GSE206039	Other	Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.	pubmed:36656711		Dr Muscle3	GSM6239386	source name:Normal Back Skeletal Muscle\|tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:258 days\|transgene:n1\|cell line:n1\|model:no transgene	Dr Muscle3	Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts	Normal Back Skeletal Muscle		For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols	Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.	tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:258 days\|transgene:n1\|cell line:n1\|model:no transgene	GSM6239386	GSM6239386: Dr Muscle3; Danio rerio; RNA Seq	GSM6239386 r1	GSM6239386	1	For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP379972		A374-A375T24.R1.fastq.gz A374-A375T24.R2.fastq.gz	fastq fastq	2203662672.0	21604536.0	GSM6239386 r1	0:51 1:51	A:564768913;C:546327011;G:532582494;T:559523522;N:460732	51	51	564768913	546327011	532582494	559523522	460732	SRX15691878	SRS13388279			Kendall Lab, Nationwide Children's Hospital / The Ohio State University	2	0.83261	0.82686	0.07473	0.06901	0.80493	0.80657	0.49306	0.49193	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-06-13	Undetermined	Embryo	Muscle	Muscular System
70275	70275	SRR19641876	SRX15691877	SRS13388278	SRP379972	PRJNA848822	VGLL2 NCOA2 leverages developmental programs for pediatric sarcomagenesis	GSE206039	Other	Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators VGLL2 NCOA2 found in infantile rhabdomyosarcoma. To delineate VGLL2 NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities we implemented a cross species comparative oncology approach with zebrafish mouse allograft and patient samples. We found that VGLL2 NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2 NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2 NCOA2 developmental targets including a RAS family GTPase arf6/ARF6. In VGLL2 NCOA2 zebrafish mouse allograft and patient tumors arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2 NCOA2 is an oncogene which leverages developmental programs for tumorigenesis and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity. Overall design: Examination of RNA seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2 NCOA2 expression and a comparison to mature zebrafish skeletal muscle and CIC DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2 NCOA2 and allografted to generate tumor models. These are compared to allografts of C2C12 empty controls.	pubmed:36656711		Dr Muscle2	GSM6239385	source name:Normal Back Skeletal Muscle\|tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:258 days\|transgene:n1\|cell line:n1\|model:no transgene	Dr Muscle2	Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp Reads were aligned with STAR 2.7.2b against the zebrafish genome danRer11 or the mouse genome mm10 Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R Read counts were normalized in R using EdgeR All code used in processing is available at https://github.com/MVesuviusC/2022 VGLL2 NCOA2 paper Assembly: danRer11 or mm10 Supplementary files format and content: geneCountsCombinedDr norm.txt.gz and geneCountsCombinedDr norm.txt.gz are tables containing normalized gene counts	Normal Back Skeletal Muscle		For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols	Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish Gateway cloning was performed to generate CMV GFP2A VGLL2NCOA2 and BetaActin GFP2A CICDUX4 injection constructs each containing the human form of the fusion oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage and fish were monitored for tumor formation. For our mouse allograft models C2C12 cells were grown in DMEM+20% FBS and were stably transfected with pcDNA3.1 control or pcDNA3.1 VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2 NCOA2 tumor models.	tissue:Normal Back Skeletal Muscle\|genotype:Wildtype AB/TL\|age at sac:258 days\|transgene:n1\|cell line:n1\|model:no transgene	GSM6239385	GSM6239385: Dr Muscle2; Danio rerio; RNA Seq	GSM6239385 r1	GSM6239385	1	For zebrafish GFP positive and thus transgene positive tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP379972		A374-A375T23.R1.fastq.gz A374-A375T23.R2.fastq.gz	fastq fastq	2450088960.0	24020480.0	GSM6239385 r1	0:51 1:51	A:646598229;C:592770801;G:584212215;T:625999341;N:508374	51	51	646598229	592770801	584212215	625999341	508374	SRX15691877	SRS13388278			Kendall Lab, Nationwide Children's Hospital / The Ohio State University	2	0.9278	0.92032	0.09971	0.09347	0.80986	0.81028	0.51973	0.52123	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-06-13	Undetermined	Embryo	Muscle	Muscular System
72661	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 o…			18 M4 24 NoRad	GSM6927792	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72662	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 o…			18 M3 24 NoRad	GSM6927791	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72663	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 o…			18 M1 24 Rad	GSM6927790	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72664	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 o…			18 F1 24 Rad	GSM6927789	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72665	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 o…			18 M2 24 Rad	GSM6927788	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72666	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 o…			28.5 F3 Ctrl NoRad	GSM6927787	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72667	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 o…			28.5 F7 Ctrl NoRad	GSM6927786	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72668	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 o…			28.5 F1 Ctrl Rad	GSM6927785	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72669	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 o…			28.5 F2 Ctrl Rad	GSM6927784	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System
72670	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 o…			28.5 F7 Ctrl Rad	GSM6927783	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 µM for 10 days to reduce locomotion and arousal. A reduced temperature group 18.5 Ctrl received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group 18.5 mel was established with a 10°C reduction in ambient temperature and the addition of 24 µM 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’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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP416971	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	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	United Kingdom	2023-01-11	Undetermined	Undetermined	Muscle	Muscular System

Advanced export

JSON shape: default, array, newline-delimited

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