run_metadata: 42185
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 42185 | SRR5482149 | SRX2765563 | SRS2149767 | SRP105243 | PRJNA383986 | Danio rerio Raw sequence reads | PRJNA383986 | Other | The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species. | Danio rerio: Large harvested line biological replicate 1 F5 offspring originating from wild caught population | LS1 F5 | breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal | RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals | LS1 F5 | LS1 F5 | Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library. | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP105243 | LS1-15_FCC4C3HACXX_L1_WHZEBagiNBANRAAPEI-215_1.fq.gz LS1-2_FCC4BJ2ACXX_L5_WHZEBagiNBABRAAPEI-202_1.fq.gz LS1-6_FCC4BJ2ACXX_L6_WHZEBagiNBAFRAAPEI-207_1.fq.gz LS1-8_FCC4BJ2ACXX_L8_WHZEBagiNBAJRAAPEI-211_1.fq.gz | fastq fastq fastq fastq | 12776192331.0 | 260738619.0 | LS1 2 FCC4BJ2ACXX L5 WHZEBagiNBABRAAPEI 202 1.fq.gz | 0:49 | A:3371838433;C:3025006624;G:2934135898;T:3444117388;N:1093988 | 49 | 3371838433 | 3025006624 | 2934135898 | 3444117388 | 1093988 | SRX2765563 | SRS2149767 | SRA557107 | University of Turku|Biology | University of Turku | 1 | 0.88482 | 0.04932 | 0.813 | 0.51224 | 49 | B | usable mapping rate | illumina | hiseq_era | unknown | other | unknown | bulk | unknown | unknown | Finland | 2017-12-04 | Juvenile | Juvenile | Liver | Liver and Biliary System |