run_metadata: 69547
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 69547 | SRR18885363 | SRX14963958 | SRS12714093 | SRP371679 | PRJNA830699 | Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle. | GSE201273 | Transcriptome Analysis | Gene expression profile was investigated using zebrafish muscle unger fasting refeeding conditions. This study revealed fasting refeeding responsive genes in zebrafish muscle. Overall design: Zebrafish muscle under the fasting for 24 hours or refeeding post 3 or 8 hours conditions were analysed using mRNA sequencing. | pubmed:35684038 | Refed 3h rep 1 [RUN 048 05] | GSM6057156 | source name:Zebrafish muscle between anus and caudal tail fin|strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours | Refed 3h rep 1 [RUN 048 05] | RNA seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings. A statistical differential expression test was used "Differential Expression for RNA Seq tool" in the CLC software. Assembly: GRCz11 genome assembly Supplementary files format and content: Excel file of statistic test and expression data. | Zebrafish muscle between anus and caudal tail fin | The following 3 experimental conditions were set for zebrafish: 24 hour fasting group Fast 3 hour refeeding group Refed 3h and 8 hour refeeding group Refed 8h. | RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. | Standard protocol. | strain:Not applicable|tissue:Muscle|age:2 month 3 month|genotype:Wild type|treatment:refeeding post 3 hours | GSM6057156 | GSM6057156: Refed 3h rep 1 [RUN 048 05]; Danio rerio; RNA Seq | GSM6057156 r1 | GSM6057156 | 1 | RNA were extracted from the muscle between the anus and caudal tail fin using RNAiso Blood Cat#9112; Takara Bio Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext PolyA mRNA Magnetic Isolation Module Cat# E7770 and E7490; New England Biolabs. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP371679 | RUN-048-05_R1.fastq RUN-048-05_R2.fastq | fastq fastq | 1458335376.0 | 20254658.0 | GSM6057156 r1 | 0:36 1:36 | A:396310547;C:324897481;G:339230815;T:397368771;N:527762 | 36 | 36 | 396310547 | 324897481 | 339230815 | 397368771 | 527762 | SRX14963958 | SRS12714093 | SRA1408267 | University of tsukuba | University of tsukuba | 2 | 0.91692 | 0.91722 | 0.0823 | 0.08538 | 0.77287 | 0.77431 | 0.53419 | 0.50913 | 36 | 36 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | nebnext | bulk | unknown | unknown | Japan | 2022-04-22 | Multi-stage | Multi-stage | Muscle | Muscular System |