{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Multi-stage\" and tissue_curation_coarse = \"Muscular System\"", "rows": [[52173, "SRR10902874", "SRX7571044", "SRS6006645", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.", null, "pubmed:34660600", null, "muscle 2", "GSM4274620", null, "source name:muscle|strain:Tubingen|tissue:muscle|genotype:wild type", "muscle 2", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.", "muscle", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:muscle|genotype:wild type", "GSM4274620", "GSM4274620: muscle 2; Danio rerio; RNA Seq", "GSM4274620", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM4274620", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:GRCz10|intentional duplicate", "muscle2.bam", "bam", 16930081042.0, 56059871.0, "GSM4274620 r1", "0:151 1:151", "A:4603243415;C:3058165767;G:2976076252;T:6287916322;N:4679286", 151, 151, null, null, 4603243415, 3058165767, 2976076252, 6287916322, 4679286, "SRX7571044", "SRS6006645", "SRA880843", "GEO", "Zhejiang University", 2, 3e-05, 0.62236, 0.0, 0.0478, 0.99997, 0.86547, 1.0, 0.64653, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2020-01-16", "Undetermined", "Multi-stage", "Muscle", "Muscular System"], [52174, "SRR10902873", "SRX7571043", "SRS6006644", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.", null, "pubmed:34660600", null, "muscle 1", "GSM4274619", null, "source name:muscle|strain:Tubingen|tissue:muscle|genotype:wild type", "muscle 1", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.", "muscle", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|tissue:muscle|genotype:wild type", "GSM4274619", "GSM4274619: muscle 1; Danio rerio; RNA Seq", "GSM4274619", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM4274619", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP194254", null, "assembly:GRCz10|intentional duplicate", "muscle1.bam", "bam", 16720405462.0, 55365581.0, "GSM4274619 r1", "0:151 1:151", "A:4156663457;C:3083564895;G:3052902778;T:6423378000;N:3896332", 151, 151, null, null, 4156663457, 3083564895, 3052902778, 6423378000, 3896332, "SRX7571043", "SRS6006644", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.65433, 0.0, 0.02201, 1.0, 0.88237, null, 0.6721, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2020-01-16", "Undetermined", "Multi-stage", "Muscle", "Muscular System"], [52184, "SRR9058963", "SRX5835163", "SRS4761459", "SRP194254", "PRJNA540466", "Characterization of the zebrafish cell landscape at single cell resolution", "GSE130487", "Transcriptome Analysis", "Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.", null, "pubmed:34660600", null, "Muscle2", "GSM3768160", null, "source name:muscle|strain:Tubingen|genotype/variation:wild type|tissue:muscle", "Muscle2", "Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.", "muscle", null, "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", null, "strain:Tubingen|genotype/variation:wild type|tissue:muscle", "GSM3768160", "GSM3768160: Muscle2; Danio rerio; RNA Seq", "GSM3768160", null, "1", "Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol", "GEO Accession:GSM3768160", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP194254", null, "assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index", "Muscle2.bam", "bam", 23974175100.0, 79913917.0, "GSM3768160 r1", "0:150 1:150", "A:5944663891;C:3921811959;G:4069898582;T:10035651088;N:2149580", 150, 150, null, null, 5944663891, 3921811959, 4069898582, 10035651088, 2149580, "SRX5835163", "SRS4761459", "SRA880843", "GEO", "Zhejiang University", 2, 0.0, 0.73445, 0.0, 0.02498, 1.0, 0.85267, null, 0.59746, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "microwellseq", null, "China", "2019-05-15", "Undetermined", "Multi-stage", "Muscle", "Muscular System"], [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. 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 1 [RUN 048 01]", "GSM6057152", 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 1 [RUN 048 01]", "RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used \"Differential Expression for RNA Seq tool\" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data.", "Zebrafish muscle between anus and caudal tail fin", "The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast  3 hour refeeding group Refed 3h  and 8 hour refeeding group Refed 8h.", "RNA were extracted from the muscle between the anus and caudal tail fin  using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina  and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.", "Standard protocol.", "strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:fasting for 24 hours", "GSM6057152", "GSM6057152: Fast rep 1 [RUN 048 01]; Danio rerio; RNA Seq", "GSM6057152 r1", "GSM6057152", "1", "RNA were extracted from the muscle between the anus and caudal tail fin  using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina  and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP371679", null, null, "RUN-048-01_R1.fastq RUN-048-01_R2.fastq", "fastq fastq", 1399856040.0, 19442445.0, "GSM6057152 r1", "0:36 1:36", "A:379554127;C:319762134;G:315409200;T:384629510;N:501069", 36, 36, null, null, 379554127, 319762134, 315409200, 384629510, 501069, "SRX14963954", "SRS12714089", "SRA1408267", "University of tsukuba", "University of tsukuba", 2, 0.9235, 0.92237, 0.08455, 0.08606, 0.74162, 0.7445, 0.53255, 0.5281, 36, 36, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2022-04-22", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"]], "truncated": false, "filtered_table_rows_count": 30, "expanded_columns": [], 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