run_metadata: 9356
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9356 | ERR2983452 | ERX2986068 | ERS2955656 | ERP112513 | PRJEB30097 | RNA Seq of Danionine species | E-MTAB-7476 | Transcriptome Analysis | Tissues specific transcriptomes of Danio rerio Danio albolineatus and Danio aesculapii Brain Liver and Gonads. | ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05 | Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. | R3wB | SAMEA5147911 | University of Hamburg, Institute of Zoology, Molecular Animal Physiology | ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147911|INSDC center name:University of Hamburg Institute of Zoology Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R3wB|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:3|organism part:brain|sample name:E MTAB 7476:R3wB|scientific name:Danio rerio|sex:female|strain:tu | Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species | E MTAB 7476:R3wB p | R3wB p | RNA Seq of Danionine species | Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. | Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:brain | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP112513 | Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species | ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05 | FCHNW2WBBXX_L6_HKZEBodsEAABRAAPEI-205_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAABRAAPEI-205_2.fq.gz | fastq fastq | 3622698000.0 | 18113490.0 | E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAABRAAPEI 205 | 0:100 1:100 | A:988454110;C:825179148;G:816134465;T:992141776;N:788501 | 100 | 100 | 988454110 | 825179148 | 816134465 | 992141776 | 788501 | ERX2986068 | ERS2955656 | ERA1674470 | University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive | University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive | 2 | 0.9287 | 0.92856 | 0.14723 | 0.14721 | 0.6928 | 0.69469 | 0.4956 | 0.49616 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Germany | 2018-12-05 | Adult | Adult | Brain | Nervous System |