run_metadata: 7948
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 7948 | ERR015562 | ERX005932 | ERS012705 | ERP000263 | PRJEB2208 | Zebrafish gene three prime end pull down for genome annotation | E-MTAB-308 | Transcriptome Analysis | E MTAB 308:Zebrafish embryo 1 dpf 2 | SAMEA898401 | Wellcome Sanger Institute | Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. 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 resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio | Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation | E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 1 dpf three prime pull down paired end 250 to 300 bp insert | Zebrafish embro 1 dpf mRNA three prime end | Zebrafish gene three prime end pull down for genome annotation | 20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp. | Experimental Factor: AGE:1 d|Experimental Factor: DEVELOPMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism|Experimental Factor: SEX:unknown sex | RNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina Genome Analyzer II | ERP000263 | Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation | ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16 | 3444_1.srf | srf | 1358041568.0 | 8934484.0 | E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 1 dpf three prime pull down paired end 250 to 300 bp insert | 0:76 1:76 | A:376045982;C:281568469;G:271365867;T:407279179;N:21782071 | 76 | 76 | 376045982 | 281568469 | 271365867 | 407279179 | 21782071 | ERX005932 | ERS012705 | ERA010603 | SC|Wellcome Trust Sanger Institute | SC|Wellcome Trust Sanger Institute | 2 | 0.94607 | 0.94542 | 0.3002 | 0.30139 | 0.73584 | 0.74038 | 0.51058 | 0.51233 | 76 | 76 | B | B | biological fallback assumption | illumina | early_illumina | 3prime | other | unknown | bulk | unknown | unknown | United Kingdom | 2010-08-19 | Pharyngula | Embryo | Whole Organism | All anatomical structures |