run_metadata: 38417
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 |
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| 38417 | SRR1821822 | SRX893423 | SRS859543 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | liver204 36m 3.75nM roten1 8w rep2 | GSM1620969 | source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks | liver204 36m 3.75nM roten1 8w rep2 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from liver | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks | GSM1620969 | GSM1620969: liver204 36m 3.75nM roten1 8w rep2; Danio rerio; RNA Seq | GSM1620969 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620969 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | Liver204.fastq.gz | fastq | 2852874500.0 | 57057490.0 | GSM1620969 r1 | 0:50 | A:758952474;C:670213462;G:651059038;T:770418307;N:2231219 | 50 | 758952474 | 670213462 | 651059038 | 770418307 | 2231219 | SRX893423 | SRS859543 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.92602 | 0.0709 | 0.78319 | 0.55468 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Liver | Liver and Biliary System |