run_metadata: 39686
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 39686 | SRR2047225 | SRX1045363 | SRS950607 | SRP058956 | PRJNA285515 | Danio rerio shield stage transcriptome | PRJNA285515 | Transcriptome Analysis | Matched RNA seq to ribosome profiling | Matched to ribosome profiling experiments in SAMN02087561 | Danio rerio Shield Stage Embryos RNA Seq | Shield Stage Embryos | strain:TLAB|dev stage:Shield|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal | Shield Stage Embryos matched to Ribosome Profiling | Shield Stage Embryos | 1 | Standard multiplexed paired end RNA Seq on the Broad Institute platform. | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP058956 | RPF-RNASeq_Shield_1_L.fastq.gz RPF-RNASeq_Shield_3_R.fastq.gz RPF-RNASeq_Shield_3_L.fastq.gz RPF-RNASeq_Shield_2_R.fastq.gz RPF-RNASeq_Shield_2_L.fastq.gz RPF-RNASeq_Shield_1_R.fastq.gz | fastq fastq fastq fastq fastq fastq | 7345884728.0 | 48328189.0 | Shield Stage Embryos | 0:76 1:76 | A:1932619942;C:1748899064;G:1767113490;T:1895258511;N:1993721 | 76 | 76 | 1932619942 | 1748899064 | 1767113490 | 1895258511 | 1993721 | SRX1045363 | SRS950607 | SRA270772 | Harvard University|Schier | Harvard University | 2 | 0.94974 | 0.95573 | 0.08627 | 0.08599 | 0.76536 | 0.76812 | 0.4916 | 0.4943 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2015-06-03 | Gastrula | Embryo | Whole Organism | All anatomical structures |