{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" and tissue_curation = \"Muscle\"", "rows": [[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.", null, "pubmed:33343615", null, "RLT rep3", "GSM3029086", null, "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\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 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\u2019s 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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C 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", null, "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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029086", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "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, null, null, 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", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [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.", null, "pubmed:33343615", null, "RLT rep2", "GSM3029085", null, "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\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 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\u2019s 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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C 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", null, "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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "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, null, null, 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", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [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.", null, "pubmed:33343615", null, "RLT rep1", "GSM3029084", null, "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\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 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\u2019s 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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C 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", null, "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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029084", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "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, null, null, 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", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [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.", null, "pubmed:33343615", null, "WT rep3", "GSM3029083", null, "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\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 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\u2019s 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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C 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", null, "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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "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, null, null, 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", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [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.", null, "pubmed:33343615", null, "WT rep2", "GSM3029082", null, "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\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 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\u2019s 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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C 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", null, "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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "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, null, null, 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", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [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.", null, "pubmed:33343615", null, "WT rep1", "GSM3029081", null, "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\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 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\u2019s 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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C 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", null, "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\uff08H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "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, null, null, 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", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0WT S C RNA Seq", "GSM3910338", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 202991469, 183350303, 181337685, 217696201, 85032, "SRX6374057", "SRS5034866", "SRA914604", "GEO", "University of Bern", 1, 0.93791, null, 0.05606, null, 0.75144, null, 0.53237, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0WT S B RNA Seq", "GSM3910337", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 271421784, 242201012, 237079646, 286766535, 112865, "SRX6374056", "SRS5034865", "SRA914604", "GEO", "University of Bern", 1, 0.93385, null, 0.05579, null, 0.73602, null, 0.50008, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0WT S 7 RNA Seq", "GSM3910336", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 236551279, 210199570, 206723666, 247589765, 97305, "SRX6374055", "SRS5034864", "SRA914604", "GEO", "University of Bern", 1, 0.93688, null, 0.05977, null, 0.80119, null, 0.50443, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0WT S 6 RNA Seq", "GSM3910335", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 297191939, 247117436, 237870203, 292953815, 115366, "SRX6374054", "SRS5034863", "SRA914604", "GEO", "University of Bern", 1, 0.89528, null, 0.06728, null, 0.78634, null, 0.53098, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0WT DD 4 RNA Seq", "GSM3910334", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 241201134, 204122008, 208735432, 252853431, 97597, "SRX6374053", "SRS5034862", "SRA914604", "GEO", "University of Bern", 1, 0.91061, null, 0.05033, null, 0.79545, null, 0.54457, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0WT DD 3 RNA Seq", "GSM3910333", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 264389932, 233507692, 235911726, 279216160, 109788, "SRX6374052", "SRS5034861", "SRA914604", "GEO", "University of Bern", 1, 0.92535, null, 0.04437, null, 0.81162, null, 0.49398, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0WT DD 2 RNA Seq", "GSM3910332", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 228696407, 206617559, 191782242, 229573977, 90647, "SRX6374051", "SRS5034860", "SRA914604", "GEO", "University of Bern", 1, 0.36358, null, 0.04768, null, 0.91303, null, 0.52314, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0KO S C RNA Seq", "GSM3910331", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 193243096, 177276287, 174035790, 205777475, 81913, "SRX6374050", "SRS5034859", "SRA914604", "GEO", "University of Bern", 1, 0.94262, null, 0.05429, null, 0.75741, null, 0.51196, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0KO S B RNA Seq", "GSM3910330", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 223023468, 203743702, 200457097, 235595080, 93003, "SRX6374049", "SRS5034858", "SRA914604", "GEO", "University of Bern", 1, 0.9374, null, 0.04142, null, 0.73111, null, 0.47223, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0KO S A RNA Seq", "GSM3910329", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 195880291, 183023619, 178202819, 210507113, 83242, "SRX6374048", "SRS5034857", "SRA914604", "GEO", "University of Bern", 1, 0.93312, null, 0.04579, null, 0.72906, null, 0.48412, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0KO S 6 RNA Seq", "GSM3910328", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 257642647, 225459692, 225710033, 263073969, 104911, "SRX6374047", "SRS5034856", "SRA914604", "GEO", "University of Bern", 1, 0.9235, null, 0.05678, null, 0.7779, null, 0.51447, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0KO DD 7 RNA Seq", "GSM3910327", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 212421329, 192524361, 192658987, 224881911, 89760, "SRX6374046", "SRS5034855", "SRA914604", "GEO", "University of Bern", 1, 0.95061, null, 0.04831, null, 0.78013, null, 0.52246, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0KO DD 6 RNA Seq", "GSM3910326", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 228413430, 209052461, 205760159, 240648496, 97030, "SRX6374045", "SRS5034854", "SRA914604", "GEO", "University of Bern", 1, 0.93764, null, 0.04361, null, 0.74777, null, 0.45055, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0KO DD 3 RNA Seq", "GSM3910325", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 244456092, 219466128, 219111604, 252630825, 101813, "SRX6374044", "SRS5034853", "SRA914604", "GEO", "University of Bern", 1, 0.90131, null, 0.0466, null, 0.83477, null, 0.50178, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [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\u00b0C.", null, "pubmed:32496654", null, "S0KO DD 2 RNA Seq", "GSM3910324", null, "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 \u201ccounts\u201d. 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\u00b0C. 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", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at 80\u00b0C. 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", null, "SRP212268", null, null, "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, null, null, null, 223803666, 200893790, 201657972, 237709184, 92546, "SRX6374043", "SRS5034852", "SRA914604", "GEO", "University of Bern", 1, 0.9298, null, 0.0537, null, 0.82574, null, 0.51143, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69540, "SRR18885356", "SRX14963965", "SRS12714100", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Refed 8h rep 4 [RUN 048 12]", "GSM6057163", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69541, "SRR18885357", "SRX14963964", "SRS12714099", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Refed 8h rep 3 [RUN 048 11]", "GSM6057162", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69542, "SRR18885358", "SRX14963963", "SRS12714098", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Refed 8h rep 2 [RUN 048 10]", "GSM6057161", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69543, "SRR18885359", "SRX14963962", "SRS12714097", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Refed 8h rep 1 [RUN 048 09]", "GSM6057160", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69544, "SRR18885360", "SRX14963961", "SRS12714096", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Refed 3h rep 4 [RUN 048 08]", "GSM6057159", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69545, "SRR18885361", "SRX14963960", "SRS12714095", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Refed 3h rep 3 [RUN 048 07]", "GSM6057158", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69546, "SRR18885362", "SRX14963959", "SRS12714094", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Refed 3h rep 2 [RUN 048 06]", "GSM6057157", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69547, "SRR18885363", "SRX14963958", "SRS12714093", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Refed 3h rep 1 [RUN 048 05]", "GSM6057156", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69548, "SRR18885364", "SRX14963957", "SRS12714092", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Fast rep 4 [RUN 048 04]", "GSM6057155", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69549, "SRR18885365", "SRX14963956", "SRS12714091", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Fast rep 3 [RUN 048 03]", "GSM6057154", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69550, "SRR18885366", "SRX14963955", "SRS12714090", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding 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.", null, "pubmed:35684038", null, "Fast rep 2 [RUN 048 02]", "GSM6057153", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "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, null, null, 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", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [69551, "SRR18885367", "SRX14963954", "SRS12714089", "SRP371679", "PRJNA830699", "Gene expression profile showing novel insight for fasting\u2013refeeding response in zebrafish muscle.", "GSE201273", "Transcriptome Analysis", "Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. 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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 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