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33 rows where devstage_curation = "Multi-stage" and tissue_curation_coarse = "Muscular System"

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technology 2

experiment.library_layout 2

devstage_curation_coarse 2

tissue_curation_coarse 1

  • Muscular System · 33 ✖

tissue_curation 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

devstage_curation 1

  • Multi-stage · 33 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
47641 47641 SRR6798780 SRX3757617 SRS3013125 SRP133827 PRJNA436713 Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish GSE111359 Transcriptome Analysis Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.   pubmed:33343615   RLT rep3 GSM3029086   source name:muscle tissues|tissue:muscle|treatment:radicicol RLT rep3 Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3’ ends of the reads and the trimmed reads were filtered with read length ≥ 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene muscle tissues Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO. Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged. tissue:muscle|treatment:radicicol GSM3029086 GSM3029086: RLT rep3; Danio rerio; RNA Seq GSM3029086   1 Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029086 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     WT3_1.fq.gz WT3_2.fq.gz fastq fastq 8153906700.0 27179689.0 GSM3029086 r1 0:150 1:150 A:1876474081;C:2211352217;G:2118339495;T:1947510591;N:230316 150 150     1876474081 2211352217 2118339495 1947510591 230316 SRX3757617 SRS3013125 SRA663830 GEO School of basic medicine science, Zhejiang University 2 0.93476 0.93504 0.13893 0.13499 0.82913 0.83487 0.53361 0.54372 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47642 47642 SRR6798779 SRX3757616 SRS3013124 SRP133827 PRJNA436713 Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish GSE111359 Transcriptome Analysis Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.   pubmed:33343615   RLT rep2 GSM3029085   source name:muscle tissues|tissue:muscle|treatment:radicicol RLT rep2 Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3’ ends of the reads and the trimmed reads were filtered with read length ≥ 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene muscle tissues Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO. Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged. tissue:muscle|treatment:radicicol GSM3029085 GSM3029085: RLT rep2; Danio rerio; RNA Seq GSM3029085   1 Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029085 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     WT2_1.fq.gz WT2_2.fq.gz fastq fastq 7278822000.0 24262740.0 GSM3029085 r1 0:150 1:150 A:1623249687;C:2023479004;G:1940623122;T:1691262512;N:207675 150 150     1623249687 2023479004 1940623122 1691262512 207675 SRX3757616 SRS3013124 SRA663830 GEO School of basic medicine science, Zhejiang University 2 0.94445 0.94327 0.112 0.10647 0.83591 0.84226 0.5112 0.52155 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47643 47643 SRR6798778 SRX3757615 SRS3013123 SRP133827 PRJNA436713 Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish GSE111359 Transcriptome Analysis Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.   pubmed:33343615   RLT rep1 GSM3029084   source name:muscle tissues|tissue:muscle|treatment:radicicol RLT rep1 Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3’ ends of the reads and the trimmed reads were filtered with read length ≥ 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene muscle tissues Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO. Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged. tissue:muscle|treatment:radicicol GSM3029084 GSM3029084: RLT rep1; Danio rerio; RNA Seq GSM3029084   1 Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029084 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     WT1_1.fq.gz WT1_2.fq.gz fastq fastq 8127579000.0 27091930.0 GSM3029084 r1 0:150 1:150 A:1936609330;C:2121138923;G:2083423270;T:1986178311;N:229166 150 150     1936609330 2121138923 2083423270 1986178311 229166 SRX3757615 SRS3013123 SRA663830 GEO School of basic medicine science, Zhejiang University 2 0.66403 0.66289 0.14695 0.14227 0.82503 0.82958 0.54774 0.55661 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47644 47644 SRR6798777 SRX3757614 SRS3013122 SRP133827 PRJNA436713 Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish GSE111359 Transcriptome Analysis Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.   pubmed:33343615   WT rep3 GSM3029083   source name:muscle tissues|tissue:muscle|treatment:DMSO WT rep3 Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3’ ends of the reads and the trimmed reads were filtered with read length ≥ 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene muscle tissues Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO. Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged. tissue:muscle|treatment:DMSO GSM3029083 GSM3029083: WT rep3; Danio rerio; RNA Seq GSM3029083   1 Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029083 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     RLT3_1.fq.gz RLT3_2.fq.gz fastq fastq 7458295500.0 24860985.0 GSM3029083 r1 0:150 1:150 A:1875422371;C:1858400851;G:1819493497;T:1904874518;N:104263 150 150     1875422371 1858400851 1819493497 1904874518 104263 SRX3757614 SRS3013122 SRA663830 GEO School of basic medicine science, Zhejiang University 2 0.88642 0.88696 0.1881 0.18533 0.79537 0.80073 0.50351 0.48568 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47645 47645 SRR6798776 SRX3757613 SRS3013120 SRP133827 PRJNA436713 Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish GSE111359 Transcriptome Analysis Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.   pubmed:33343615   WT rep2 GSM3029082   source name:muscle tissues|tissue:muscle|treatment:DMSO WT rep2 Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3’ ends of the reads and the trimmed reads were filtered with read length ≥ 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene muscle tissues Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO. Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged. tissue:muscle|treatment:DMSO GSM3029082 GSM3029082: WT rep2; Danio rerio; RNA Seq GSM3029082   1 Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029082 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     RLT2_2.fq.gz RLT2_1.fq.gz fastq fastq 9462767100.0 31542557.0 GSM3029082 r1 0:150 1:150 A:2301678607;C:2445064584;G:2361534540;T:2354357373;N:131996 150 150     2301678607 2445064584 2361534540 2354357373 131996 SRX3757613 SRS3013120 SRA663830 GEO School of basic medicine science, Zhejiang University 2 0.91337 0.91337 0.17924 0.17526 0.78317 0.79011 0.50203 0.51647 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
47646 47646 SRR6798775 SRX3757612 SRS3013121 SRP133827 PRJNA436713 Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish GSE111359 Transcriptome Analysis Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.   pubmed:33343615   WT rep1 GSM3029081   source name:muscle tissues|tissue:muscle|treatment:DMSO WT rep1 Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3’ ends of the reads and the trimmed reads were filtered with read length ≥ 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene muscle tissues Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO. Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. Breeding fish were maintained at 28°C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged. tissue:muscle|treatment:DMSO GSM3029081 GSM3029081: WT rep1; Danio rerio; RNA Seq GSM3029081   1 Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads. GEO Accession:GSM3029081 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP133827     RLT1_1.fq.gz RLT1_2.fq.gz fastq fastq 7599797400.0 25332658.0 GSM3029081 r1 0:150 1:150 A:1883972109;C:1921348946;G:1869717767;T:1924652451;N:106127 150 150     1883972109 1921348946 1869717767 1924652451 106127 SRX3757612 SRS3013121 SRA663830 GEO School of basic medicine science, Zhejiang University 2 0.88692 0.88623 0.18432 0.18166 0.79928 0.80693 0.50362 0.5124 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2018-03-02 Multi-stage Embryo Muscle Muscular System
52955 52955 SRR9610848 SRX6374057 SRS5034866 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0WT S C RNA Seq GSM3910338   source name:WT Standard Diet Muscle|Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle S0WT S C RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. WT Standard Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle GSM3910338 GSM3910338: S0WT S C RNA Seq; Danio rerio; RNA Seq GSM3910338   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910338 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0WT_S_C__RNA_Seq_Directional_S46_L005_R1_001.fastq.gz fastq 785460690.0 15401190.0 GSM3910338 r1 0:51 A:202991469;C:183350303;G:181337685;T:217696201;N:85032 51       202991469 183350303 181337685 217696201 85032 SRX6374057 SRS5034866 SRA914604 GEO University of Bern 1 0.93791   0.05606   0.75144   0.53237   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52956 52956 SRR9610847 SRX6374056 SRS5034865 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0WT S B RNA Seq GSM3910337   source name:WT Standard Diet Muscle|Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle S0WT S B RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. WT Standard Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle GSM3910337 GSM3910337: S0WT S B RNA Seq; Danio rerio; RNA Seq GSM3910337   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910337 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0WT_S_B__RNA_Seq_Directional_S45_L005_R1_001.fastq.gz fastq 1037581842.0 20344742.0 GSM3910337 r1 0:51 A:271421784;C:242201012;G:237079646;T:286766535;N:112865 51       271421784 242201012 237079646 286766535 112865 SRX6374056 SRS5034865 SRA914604 GEO University of Bern 1 0.93385   0.05579   0.73602   0.50008   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52957 52957 SRR9610846 SRX6374055 SRS5034864 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0WT S 7 RNA Seq GSM3910336   source name:WT Standard Diet Muscle|Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle S0WT S 7 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. WT Standard Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle GSM3910336 GSM3910336: S0WT S 7 RNA Seq; Danio rerio; RNA Seq GSM3910336   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910336 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0WT_S_7__RNA_Seq_Directional_S48_L005_R1_001.fastq.gz fastq 901161585.0 17669835.0 GSM3910336 r1 0:51 A:236551279;C:210199570;G:206723666;T:247589765;N:97305 51       236551279 210199570 206723666 247589765 97305 SRX6374055 SRS5034864 SRA914604 GEO University of Bern 1 0.93688   0.05977   0.80119   0.50443   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52958 52958 SRR9610845 SRX6374054 SRS5034863 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0WT S 6 RNA Seq GSM3910335   source name:WT Standard Diet Muscle|Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle S0WT S 6 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. WT Standard Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle GSM3910335 GSM3910335: S0WT S 6 RNA Seq; Danio rerio; RNA Seq GSM3910335   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910335 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0WT_S_6__RNA_Seq_Directional_S47_L005_R1_001.fastq.gz fastq 1075248759.0 21083309.0 GSM3910335 r1 0:51 A:297191939;C:247117436;G:237870203;T:292953815;N:115366 51       297191939 247117436 237870203 292953815 115366 SRX6374054 SRS5034863 SRA914604 GEO University of Bern 1 0.89528   0.06728   0.78634   0.53098   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52959 52959 SRR9610844 SRX6374053 SRS5034862 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0WT DD 4 RNA Seq GSM3910334   source name:WT Double Diet Muscle|Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle S0WT DD 4 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. WT Double Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle GSM3910334 GSM3910334: S0WT DD 4 RNA Seq; Danio rerio; RNA Seq GSM3910334   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910334 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0WT_DD_4__RNA_Seq_Directional_S55_L005_R1_001.fastq.gz fastq 907009602.0 17784502.0 GSM3910334 r1 0:51 A:241201134;C:204122008;G:208735432;T:252853431;N:97597 51       241201134 204122008 208735432 252853431 97597 SRX6374053 SRS5034862 SRA914604 GEO University of Bern 1 0.91061   0.05033   0.79545   0.54457   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52960 52960 SRR9610843 SRX6374052 SRS5034861 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0WT DD 3 RNA Seq GSM3910333   source name:WT Double Diet Muscle|Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle S0WT DD 3 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. WT Double Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle GSM3910333 GSM3910333: S0WT DD 3 RNA Seq; Danio rerio; RNA Seq GSM3910333   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910333 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0WT_DD_3__RNA_Seq_Directional_S54_L005_R1_001.fastq.gz fastq 1013135298.0 19865398.0 GSM3910333 r1 0:51 A:264389932;C:233507692;G:235911726;T:279216160;N:109788 51       264389932 233507692 235911726 279216160 109788 SRX6374052 SRS5034861 SRA914604 GEO University of Bern 1 0.92535   0.04437   0.81162   0.49398   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52961 52961 SRR9610842 SRX6374051 SRS5034860 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0WT DD 2 RNA Seq GSM3910332   source name:WT Double Diet Muscle|Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle S0WT DD 2 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. WT Double Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle GSM3910332 GSM3910332: S0WT DD 2 RNA Seq; Danio rerio; RNA Seq GSM3910332   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910332 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0WT_DD_2__RNA_Seq_Directional_S53_L005_R1_001.fastq.gz fastq 856760832.0 16799232.0 GSM3910332 r1 0:51 A:228696407;C:206617559;G:191782242;T:229573977;N:90647 51       228696407 206617559 191782242 229573977 90647 SRX6374051 SRS5034860 SRA914604 GEO University of Bern 1 0.36358   0.04768   0.91303   0.52314   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52962 52962 SRR9610841 SRX6374050 SRS5034859 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0KO S C RNA Seq GSM3910331   source name:KO Standard Diet Muscle|Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle S0KO S C RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. KO Standard Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle GSM3910331 GSM3910331: S0KO S C RNA Seq; Danio rerio; RNA Seq GSM3910331   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910331 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0KO_S_C__RNA_Seq_Directional_S51_L005_R1_001.fastq.gz fastq 750414561.0 14714011.0 GSM3910331 r1 0:51 A:193243096;C:177276287;G:174035790;T:205777475;N:81913 51       193243096 177276287 174035790 205777475 81913 SRX6374050 SRS5034859 SRA914604 GEO University of Bern 1 0.94262   0.05429   0.75741   0.51196   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52963 52963 SRR9610840 SRX6374049 SRS5034858 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0KO S B RNA Seq GSM3910330   source name:KO Standard Diet Muscle|Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle S0KO S B RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. KO Standard Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle GSM3910330 GSM3910330: S0KO S B RNA Seq; Danio rerio; RNA Seq GSM3910330   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910330 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0KO_S_B__RNA_Seq_Directional_S50_L005_R1_001.fastq.gz fastq 862912350.0 16919850.0 GSM3910330 r1 0:51 A:223023468;C:203743702;G:200457097;T:235595080;N:93003 51       223023468 203743702 200457097 235595080 93003 SRX6374049 SRS5034858 SRA914604 GEO University of Bern 1 0.9374   0.04142   0.73111   0.47223   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52964 52964 SRR9610839 SRX6374048 SRS5034857 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0KO S A RNA Seq GSM3910329   source name:KO Standard Diet Muscle|Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle S0KO S A RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. KO Standard Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle GSM3910329 GSM3910329: S0KO S A RNA Seq; Danio rerio; RNA Seq GSM3910329   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910329 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0KO_S_A__RNA_Seq_Directional_S49_L005_R1_001.fastq.gz fastq 767697084.0 15052884.0 GSM3910329 r1 0:51 A:195880291;C:183023619;G:178202819;T:210507113;N:83242 51       195880291 183023619 178202819 210507113 83242 SRX6374048 SRS5034857 SRA914604 GEO University of Bern 1 0.93312   0.04579   0.72906   0.48412   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52965 52965 SRR9610838 SRX6374047 SRS5034856 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0KO S 6 RNA Seq GSM3910328   source name:KO Standard Diet Muscle|Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle S0KO S 6 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. KO Standard Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle GSM3910328 GSM3910328: S0KO S 6 RNA Seq; Danio rerio; RNA Seq GSM3910328   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910328 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0KO_S_6__RNA_Seq_Directional_S52_L005_R1_001.fastq.gz fastq 971991252.0 19058652.0 GSM3910328 r1 0:51 A:257642647;C:225459692;G:225710033;T:263073969;N:104911 51       257642647 225459692 225710033 263073969 104911 SRX6374047 SRS5034856 SRA914604 GEO University of Bern 1 0.9235   0.05678   0.7779   0.51447   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52966 52966 SRR9610837 SRX6374046 SRS5034855 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0KO DD 7 RNA Seq GSM3910327   source name:KO Double Diet Muscle|Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle S0KO DD 7 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. KO Double Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle GSM3910327 GSM3910327: S0KO DD 7 RNA Seq; Danio rerio; RNA Seq GSM3910327   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910327 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0KO_DD_7__RNA_Seq_Directional_S59_L005_R1_001.fastq.gz fastq 822576348.0 16128948.0 GSM3910327 r1 0:51 A:212421329;C:192524361;G:192658987;T:224881911;N:89760 51       212421329 192524361 192658987 224881911 89760 SRX6374046 SRS5034855 SRA914604 GEO University of Bern 1 0.95061   0.04831   0.78013   0.52246   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52967 52967 SRR9610836 SRX6374045 SRS5034854 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0KO DD 6 RNA Seq GSM3910326   source name:KO Double Diet Muscle|Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle S0KO DD 6 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. KO Double Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle GSM3910326 GSM3910326: S0KO DD 6 RNA Seq; Danio rerio; RNA Seq GSM3910326   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910326 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0KO_DD_6__RNA_Seq_Directional_S58_L005_R1_001.fastq.gz fastq 883971576.0 17332776.0 GSM3910326 r1 0:51 A:228413430;C:209052461;G:205760159;T:240648496;N:97030 51       228413430 209052461 205760159 240648496 97030 SRX6374045 SRS5034854 SRA914604 GEO University of Bern 1 0.93764   0.04361   0.74777   0.45055   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52968 52968 SRR9610835 SRX6374044 SRS5034853 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0KO DD 3 RNA Seq GSM3910325   source name:KO Double Diet Muscle|Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle S0KO DD 3 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. KO Double Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle GSM3910325 GSM3910325: S0KO DD 3 RNA Seq; Danio rerio; RNA Seq GSM3910325   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910325 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0KO_DD_3__RNA_Seq_Directional_S57_L005_R1_001.fastq.gz fastq 935766462.0 18348362.0 GSM3910325 r1 0:51 A:244456092;C:219466128;G:219111604;T:252630825;N:101813 51       244456092 219466128 219111604 252630825 101813 SRX6374044 SRS5034853 SRA914604 GEO University of Bern 1 0.90131   0.0466   0.83477   0.50178   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52969 52969 SRR9610834 SRX6374043 SRS5034852 SRP212268 PRJNA551601 Respiratory supercomplexes provide metabolic efficiency in zebrafish GSE133487 Transcriptome Analysis The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.   pubmed:32496654   S0KO DD 2 RNA Seq GSM3910324   source name:KO Double Diet Muscle|Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle S0KO DD 2 RNA Seq Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth. KO Double Diet Muscle Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System Zebrafish were grown at same density 13 fish in 2 l tanks Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle GSM3910324 GSM3910324: S0KO DD 2 RNA Seq; Danio rerio; RNA Seq GSM3910324   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System GEO Accession:GSM3910324 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP212268     S0KO_DD_2__RNA_Seq_Directional_S56_L005_R1_001.fastq.gz fastq 864157158.0 16944258.0 GSM3910324 r1 0:51 A:223803666;C:200893790;G:201657972;T:237709184;N:92546 51       223803666 200893790 201657972 237709184 92546 SRX6374043 SRS5034852 SRA914604 GEO University of Bern 1 0.9298   0.0537   0.82574   0.51143   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
69540 69540 SRR18885356 SRX14963965 SRS12714100 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Refed 8h rep 4 [RUN 048 12] GSM6057163   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 8 hours Refed 8h rep 4 [RUN 048 12] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 8 hours GSM6057163 GSM6057163: Refed 8h rep 4 [RUN 048 12]; Danio rerio; RNA Seq GSM6057163 r1 GSM6057163 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-12_R1.fastq RUN-048-12_R2.fastq fastq fastq 1769202432.0 24572256.0 GSM6057163 r1 0:36 1:36 A:476394817;C:400880078;G:407298919;T:483990730;N:637888 36 36     476394817 400880078 407298919 483990730 637888 SRX14963965 SRS12714100 SRA1408267 University of tsukuba University of tsukuba 2 0.92406 0.92423 0.08015 0.08247 0.7513 0.75412 0.52264 0.53361 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69541 69541 SRR18885357 SRX14963964 SRS12714099 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Refed 8h rep 3 [RUN 048 11] GSM6057162   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 8 hours Refed 8h rep 3 [RUN 048 11] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 8 hours GSM6057162 GSM6057162: Refed 8h rep 3 [RUN 048 11]; Danio rerio; RNA Seq GSM6057162 r1 GSM6057162 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-11_R1.fastq RUN-048-11_R2.fastq fastq fastq 1453859280.0 20192490.0 GSM6057162 r1 0:36 1:36 A:392437566;C:331357872;G:334413277;T:395145809;N:504756 36 36     392437566 331357872 334413277 395145809 504756 SRX14963964 SRS12714099 SRA1408267 University of tsukuba University of tsukuba 2 0.92535 0.92228 0.07767 0.08251 0.76621 0.77279 0.54439 0.53867 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69542 69542 SRR18885358 SRX14963963 SRS12714098 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Refed 8h rep 2 [RUN 048 10] GSM6057161   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 8 hours Refed 8h rep 2 [RUN 048 10] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 8 hours GSM6057161 GSM6057161: Refed 8h rep 2 [RUN 048 10]; Danio rerio; RNA Seq GSM6057161 r1 GSM6057161 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-10_R1.fastq RUN-048-10_R2.fastq fastq fastq 1525138272.0 21182476.0 GSM6057161 r1 0:36 1:36 A:409985793;C:342949239;G:360472653;T:411183205;N:547382 36 36     409985793 342949239 360472653 411183205 547382 SRX14963963 SRS12714098 SRA1408267 University of tsukuba University of tsukuba 2 0.92619 0.92568 0.07528 0.08014 0.77092 0.77398 0.54102 0.53845 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69543 69543 SRR18885359 SRX14963962 SRS12714097 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Refed 8h rep 1 [RUN 048 09] GSM6057160   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 8 hours Refed 8h rep 1 [RUN 048 09] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 8 hours GSM6057160 GSM6057160: Refed 8h rep 1 [RUN 048 09]; Danio rerio; RNA Seq GSM6057160 r1 GSM6057160 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-09_R1.fastq RUN-048-09_R2.fastq fastq fastq 1519378128.0 21102474.0 GSM6057160 r1 0:36 1:36 A:414652569;C:341956821;G:342903761;T:419318612;N:546365 36 36     414652569 341956821 342903761 419318612 546365 SRX14963962 SRS12714097 SRA1408267 University of tsukuba University of tsukuba 2 0.92503 0.92387 0.09235 0.09356 0.74594 0.74718 0.52935 0.5194 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69544 69544 SRR18885360 SRX14963961 SRS12714096 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Refed 3h rep 4 [RUN 048 08] GSM6057159   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours Refed 3h rep 4 [RUN 048 08] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours GSM6057159 GSM6057159: Refed 3h rep 4 [RUN 048 08]; Danio rerio; RNA Seq GSM6057159 r1 GSM6057159 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-08_R1.fastq RUN-048-08_R2.fastq fastq fastq 1679096232.0 23320781.0 GSM6057159 r1 0:36 1:36 A:454384803;C:379635124;G:387311608;T:457154317;N:610380 36 36     454384803 379635124 387311608 457154317 610380 SRX14963961 SRS12714096 SRA1408267 University of tsukuba University of tsukuba 2 0.92834 0.9276 0.07257 0.07483 0.78338 0.78626 0.53134 0.56153 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69545 69545 SRR18885361 SRX14963960 SRS12714095 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Refed 3h rep 3 [RUN 048 07] GSM6057158   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours Refed 3h rep 3 [RUN 048 07] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours GSM6057158 GSM6057158: Refed 3h rep 3 [RUN 048 07]; Danio rerio; RNA Seq GSM6057158 r1 GSM6057158 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-07_R1.fastq RUN-048-07_R2.fastq fastq fastq 1413671688.0 19634329.0 GSM6057158 r1 0:36 1:36 A:379962785;C:322083978;G:328291610;T:382829243;N:504072 36 36     379962785 322083978 328291610 382829243 504072 SRX14963960 SRS12714095 SRA1408267 University of tsukuba University of tsukuba 2 0.92704 0.92602 0.07325 0.07624 0.76928 0.77177 0.5398 0.52915 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69546 69546 SRR18885362 SRX14963959 SRS12714094 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Refed 3h rep 2 [RUN 048 06] GSM6057157   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours Refed 3h rep 2 [RUN 048 06] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours GSM6057157 GSM6057157: Refed 3h rep 2 [RUN 048 06]; Danio rerio; RNA Seq GSM6057157 r1 GSM6057157 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-06_R1.fastq RUN-048-06_R2.fastq fastq fastq 1700532360.0 23618505.0 GSM6057157 r1 0:36 1:36 A:460614187;C:381645854;G:392388519;T:465280478;N:603322 36 36     460614187 381645854 392388519 465280478 603322 SRX14963959 SRS12714094 SRA1408267 University of tsukuba University of tsukuba 2 0.92244 0.92089 0.08231 0.08503 0.76725 0.77055 0.5507 0.50797 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69547 69547 SRR18885363 SRX14963958 SRS12714093 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Refed 3h rep 1 [RUN 048 05] GSM6057156   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours Refed 3h rep 1 [RUN 048 05] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours GSM6057156 GSM6057156: Refed 3h rep 1 [RUN 048 05]; Danio rerio; RNA Seq GSM6057156 r1 GSM6057156 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-05_R1.fastq RUN-048-05_R2.fastq fastq fastq 1458335376.0 20254658.0 GSM6057156 r1 0:36 1:36 A:396310547;C:324897481;G:339230815;T:397368771;N:527762 36 36     396310547 324897481 339230815 397368771 527762 SRX14963958 SRS12714093 SRA1408267 University of tsukuba University of tsukuba 2 0.91692 0.91722 0.0823 0.08538 0.77287 0.77431 0.53419 0.50913 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69548 69548 SRR18885364 SRX14963957 SRS12714092 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Fast rep 4 [RUN 048 04] GSM6057155   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours Fast rep 4 [RUN 048 04] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours GSM6057155 GSM6057155: Fast rep 4 [RUN 048 04]; Danio rerio; RNA Seq GSM6057155 r1 GSM6057155 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-04_R1.fastq RUN-048-04_R2.fastq fastq fastq 1527486624.0 21215092.0 GSM6057155 r1 0:36 1:36 A:412438816;C:343899402;G:353167908;T:417429509;N:550989 36 36     412438816 343899402 353167908 417429509 550989 SRX14963957 SRS12714092 SRA1408267 University of tsukuba University of tsukuba 2 0.92063 0.92057 0.08147 0.08404 0.75641 0.75875 0.5198 0.52462 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69549 69549 SRR18885365 SRX14963956 SRS12714091 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Fast rep 3 [RUN 048 03] GSM6057154   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours Fast rep 3 [RUN 048 03] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours GSM6057154 GSM6057154: Fast rep 3 [RUN 048 03]; Danio rerio; RNA Seq GSM6057154 r1 GSM6057154 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-03_R1.fastq RUN-048-03_R2.fastq fastq fastq 1158403680.0 16088940.0 GSM6057154 r1 0:36 1:36 A:314469557;C:259972112;G:264644818;T:318924093;N:393100 36 36     314469557 259972112 264644818 318924093 393100 SRX14963956 SRS12714091 SRA1408267 University of tsukuba University of tsukuba 2 0.92352 0.92272 0.08987 0.0924 0.75461 0.75666 0.54466 0.54171 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69550 69550 SRR18885366 SRX14963955 SRS12714090 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Fast rep 2 [RUN 048 02] GSM6057153   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours Fast rep 2 [RUN 048 02] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours GSM6057153 GSM6057153: Fast rep 2 [RUN 048 02]; Danio rerio; RNA Seq GSM6057153 r1 GSM6057153 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-02_R1.fastq RUN-048-02_R2.fastq fastq fastq 1480092552.0 20556841.0 GSM6057153 r1 0:36 1:36 A:404353415;C:330249458;G:335093887;T:409868476;N:527316 36 36     404353415 330249458 335093887 409868476 527316 SRX14963955 SRS12714090 SRA1408267 University of tsukuba University of tsukuba 2 0.91937 0.91814 0.08608 0.08811 0.76319 0.76617 0.55183 0.5413 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System
69551 69551 SRR18885367 SRX14963954 SRS12714089 SRP371679 PRJNA830699 Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. GSE201273 Transcriptome Analysis Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing.   pubmed:35684038   Fast rep 1 [RUN 048 01] GSM6057152   source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours Fast rep 1 [RUN 048 01] RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. Zebrafish muscle between anus and caudal tail fin The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. Standard protocol. strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours GSM6057152 GSM6057152: Fast rep 1 [RUN 048 01]; Danio rerio; RNA Seq GSM6057152 r1 GSM6057152 1 RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP371679     RUN-048-01_R1.fastq RUN-048-01_R2.fastq fastq fastq 1399856040.0 19442445.0 GSM6057152 r1 0:36 1:36 A:379554127;C:319762134;G:315409200;T:384629510;N:501069 36 36     379554127 319762134 315409200 384629510 501069 SRX14963954 SRS12714089 SRA1408267 University of tsukuba University of tsukuba 2 0.9235 0.92237 0.08455 0.08606 0.74162 0.7445 0.53255 0.5281 36 36 B B biological fallback assumption illumina nextseq unknown cdna_unspecified nebnext bulk unknown unknown   Japan 2022-04-22 Multi-stage Multi-stage Muscle Muscular System

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