run_metadata: 1428
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1428 | ERR1821905 | ERX1884397 | ERS1343231 | ERP012128 | PRJEB10833 | RNASeq of zebrafish embryos infected with pathogens | RNASeq_of_zebrafish_embryos_infected_with_pathogens-sc-3907 | Transcriptome Analysis | Zebrafish embryos were challenged with a range of pathogens and their mRNA expression profiles compared to mock challenged siblings using whole embryo RNA seq | ArrayExpress:E ERAD 428 | zmp ph263 inf 6hpi 14 | SAMEA4431782 | Wellcome Sanger Institute | ArrayExpress DevelopmentalStage:Hatching:Long pec Hatching:Pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2017 02 02|ENA last update:2016 09 12|External Id:SAMEA4431782|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2017 02 02T09:08:56Z|INSDC last update:2016 09 12T10:42:05Z|INSDC status:public|Submitter Id:877182e0 74d8 11e6 a83e 3c4a9275d6c8|common name:zebrafish|sample description:Total RNA from a single zebrafish embryo from the TLF strain injected with 8nl of Salm1lla typhimurium pathogen load of 179 CFU in 2%Phenol Red in PBS at 48hpf and collected 6 hours post infection. The RNA also contains ERCC spike mix 1 Ambion.|sample name:877182e0 74d8 11e6 a83e 3c4a9275d6c8|strain:TLF | Illumina HiSeq 2500 paired end sequencing | SC EXP 21115 7#11 | DN465656V:C2 | Illumina sequencing of library DN465656V:C2 constructed from sample accession ERS1343231 for study accession ERP012128. This is part of an Illumina multiplexed sequencing run 21115 7. This submission includes reads tagged with the sequence GGCTACAG. | RNA seq dUTP eukaryotic | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | ERP012128 | Illumina HiSeq 2500 paired end sequencing | ENA FIRST PUBLIC:2017 02 07|ENA LAST UPDATE:2018 11 16 | 21115_7#11.cram | cram | 320521950.0 | 2136813.0 | SC RUN 21115 7#11 | 0:75 1:75 | A:84018705;C:75695161;G:75424320;T:85360772;N:22992 | 75 | 75 | 84018705 | 75695161 | 75424320 | 85360772 | 22992 | ERX1884397 | ERS1343231 | ERA808852 | European Nucleotide Archive | Wellcome Sanger Institute | 2 | 0.95781 | 0.96265 | 0.11883 | 0.11449 | 0.68613 | 0.68724 | 0.48729 | 0.48412 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2016-09-12 | Hatching | Embryo | Fin | Surface Structure |