run_metadata: 8064
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 8064 | ERR035545 | ERX013540 | ERS017861 | ERP000447 | PRJEB2368 | Sanger zebrafish sequencing | E-MTAB-460 | Other | Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. | Zebrafish adult brain | SAMEA782568 | Wellcome Sanger Institute | ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782568|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult brain|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:brain|sample name:E MTAB 460:Zebrafish adult brain|sex:mixed | Sanger zebrafish sequencing | E MTAB 460 part2:5625 1 | ZFbrain 2 RNA 1523492 | Sanger zebrafish sequencing | Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented LiCl precipitated reverse transcribed with random primers a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp. | Experimental Factor: ORGANISM PART:brain | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina Genome Analyzer II | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000447 | Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing | ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16 | 5625_1.srf | srf | 4576566720.0 | 28603542.0 | E MTAB 460 part2:5625 1.srf | 0:76 1:8 2:76 | A:1227184716;C:942715631;G:951021478;T:1219839320;N:6977239 | 76 | 8 | 76 | 1227184716 | 942715631 | 951021478 | 1219839320 | 6977239 | ERX013540 | ERS017861 | ERA033503 | SC|Wellcome Trust Sanger Institute | SC|Wellcome Trust Sanger Institute | 2 | 0.86503 | 0.86182 | 0.22392 | 0.22256 | 0.69664 | 0.69865 | 0.51454 | 0.51606 | 76 | 76 | B | B | biological fallback assumption | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | United Kingdom | 2011-02-03 | Adult | Adult | Brain | Nervous System |