run_metadata: 40063
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40063 | SRR2750982 | SRX1362052 | SRS1125467 | 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 brain 132 | GSM1915488 | source name:total RNA extracted from brain|strain:AB JxTu|age:24 month|age category: |tissue:brain | NH FLI brain 132 | 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 brain | 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|age:24 month|age category: |tissue:brain | GSM1915488 | GSM1915488: NH FLI brain 132; Danio rerio; RNA Seq | GSM1915488 | 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:GSM1915488 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP065208 | brain_24m_DR132.fq.gz | fastq | 2431155350.0 | 48623107.0 | GSM1915488 r1 | 0:50 | A:673834712;C:548795822;G:530868509;T:677188005;N:468302 | 50 | 673834712 | 548795822 | 530868509 | 677188005 | 468302 | SRX1362052 | SRS1125467 | SRA306458 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.92967 | 0.18591 | 0.69787 | 0.498 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2015-10-21 | Adult | Adult | Brain | Nervous System |