run_metadata: 43225
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 43225 | SRR5921089 | SRX3081916 | SRS2420562 | SRP115129 | PRJNA397733 | Sequencing of Danio rerio muscle for 2 age groups post physical exercise | GSE102430 | Transcriptome Analysis | Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples 1 year w/o physical exercise 5 samples 3 year w/ physical exercise 5 samples 3 year w/o physical exercise 5 samples | NH FLI 219 muscle RNAseq | GSM2736439 | source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel | NH FLI 219 muscle RNAseq | Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10 and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample. | muscle | Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction. | strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel | GSM2736439 | GSM2736439: NH FLI 219 muscle RNAseq; Danio rerio; RNA Seq | GSM2736439 | 1 | Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction. | GEO Accession:GSM2736439 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP115129 | 2532374300.0 | 50647486.0 | GSM2736439 r1 | 0:50 | A:663072795;C:618496710;G:602144102;T:648561930;N:98763 | 50 | 663072795 | 618496710 | 602144102 | 648561930 | 98763 | SRX3081916 | SRS2420562 | SRA597918 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.96219 | 0.03463 | 0.82412 | 0.49185 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2017-08-09 | Adult | Adult | Muscle | Muscular System |