run_metadata: 36589
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36589 | SRR1562531 | SRX204106 | SRS373224 | SRP017135 | PRJNA179237 | Danio rerio strain:SAT Transcriptome or Gene expression | PRJNA179237 | Other | Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver muscle eye brain intestine pancreas and testes was carried out along with proteomic analysis of 10 organs. | Zebrafish transcriptomic profile for Liver spleen Testes Eye Muscle Intestine Pancreas | Zebrafish trancriptome for protegenomic analysis | zebrafish IOB JHU transcriptome | Zebrafish transcriptome profiling for proteogenomic analysis | JHU IOB zebrafish RNA Seq | 1 | SRR1562528 belongs to the eye tissue SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue. | RNA-Seq | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina HiScanSQ | <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> | SRP017135 | 4394828000.0 | 45714707.0 | zebrafish data3 | 0:50 1:50 | A:1146792341;C:1067826128;G:1033443384;T:1146608253;N:157894 | 50 | 50 | 1146792341 | 1067826128 | 1033443384 | 1146608253 | 157894 | SRX204106 | SRS373224 | SRA060234 | Johns Hopkins University|Pandey Lab | Johns Hopkins University | 2 | 0.96496 | 0.95999 | 0.03952 | 0.03946 | 0.78571 | 0.78518 | 0.51359 | 0.49202 | 50 | 50 | B | B | biological fallback assumption | illumina | early_illumina | unknown | unknown | unknown | bulk | unknown | unknown | United States | 2015-07-22 | Undetermined | Undetermined | Multi-tissue | Multi-system |