run_metadata: 36695
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36695 | SRR831692 | SRX269410 | SRS415075 | SRP021210 | PRJNA197389 | Danio rerio strain:Wildtype strains AB WIK and AB/Tueb Transcriptome or Gene expression | PRJNA197389 | Transcriptome Analysis | Gene expression profiling of several wildtype strains of zebrafish embryos. The samples were pooled from several developmental stages ranging from 2 dpf to 7 dpf This breadth of sampling gives a broad idea of genes expressed during early development and SNPs associated with wildtype strains. | pubmed:23299976 | RNA seq from Fred Hutchinscon AB strain of Danio rerio | AB FH.bam | geo loc name:USA: Seattle WA|isolation source:zebrafish embryos|subspecf gen lin:AB from Fred Hutchinson|dev stage:mix of 2 dpf 7 dpf type:pool of multiple embryos from each develomental stage|strain:AB | AB FH | AB FH | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><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_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP021210 | FH_AB.bam | bam | 2246623442.0 | 24070720.0 | AB FH | 0:49 1:49 | A:574600075;C:551290408;G:541354340;T:579331239;N:47380 | 49 | 49 | 574600075 | 551290408 | 541354340 | 579331239 | 47380 | SRX269410 | SRS415075 | SRA073810 | Fred Hutchinson Cancer Research Center|Moens | Fred Hutchinson Cancer Research Center | 2 | 0.96858 | 0.96855 | 0.08369 | 0.08397 | 0.67953 | 0.67959 | 0.45983 | 0.44926 | 49 | 49 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | other | unknown | bulk | unknown | unknown | United States | 2014-04-19 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures |