run_metadata: 39999
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 39999 | SRR6081857 | SRX3220844 | SRS2545507 | SRP065208 | PRJNA299585 | Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin | GSE74244 | Transcriptome Analysis | Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group | pubmed:29382830 | NH FLI liver 93+94 | GSM2795185 | source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:6 month|age category: |tissue:liver | NH FLI liver 93+94 | Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample | total RNA extracted from skin | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | strain:AB JxTu Tgwt1a:GFP|age:6 month|age category: |tissue:liver | GSM2795185 | GSM2795185: NH FLI liver 93+94; Danio rerio; RNA Seq | GSM2795185 | 1 | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | GEO Accession:GSM2795185 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP065208 | liver_6m_DR93DR94.fq.gz | fastq | 2333496400.0 | 46669928.0 | GSM2795185 r1 | 0:50 | A:614203790;C:555535741;G:543915663;T:619744641;N:96565 | 50 | 614203790 | 555535741 | 543915663 | 619744641 | 96565 | SRX3220844 | SRS2545507 | SRA306458 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.94566 | 0.08285 | 0.68876 | 0.54555 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2017-09-27 | Adult | Adult | Liver | Liver and Biliary System |