run_metadata: 36518
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36518 | SRR578919 | SRX190977 | SRS366698 | SRP015982 | PRJNA176481 | Small RNA analysis of Tu And SJD zebrafish strain and their progeny | GSE41299 | Transcriptome Analysis | Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled . | pubmed:23335638 | TuxSJDF2 | GSM1014083 | source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary | TuxSJDF2 | Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts | Ovary | Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. | Animals were grown under standard conditioni | gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary | GSM1014083 | GSM1014083: TuxSJDF2; Danio rerio; RNA Seq | GSM1014083 1 | 1 | GEO Accession:GSM1014083 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP015982 | TuxSJDF2.fastq | fastq | 1036162620.0 | 28782295.0 | GSM1014083 r1 | 0:36 | A:268457303;C:215700792;G:273583173;T:278046713;N:374639 | 36 | 268457303 | 215700792 | 273583173 | 278046713 | 374639 | SRX190977 | SRS366698 | SRA059229 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.16399 | 0.12914 | 0.9517 | 0.52232 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2012-10-03 | Adult | Adult | Gonad | Reproductive System |