run_metadata: 7949
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 7949 | ERR015566 | ERX005931 | ERS000090 | ERP000263 | PRJEB2208 | Zebrafish gene three prime end pull down for genome annotation | E-MTAB-308 | Transcriptome Analysis | ZF ovary sample1 | SAMEA708832 | Wellcome Sanger Institute | Alias:ZF ovary sample1|Description:RNA extracted from adult zebrafish ovary|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000090|Sample Name:ERS000090|Sex:female|Strain: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 adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert | Zebrafish adult ovary 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: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:ovary|Experimental Factor: SEX:female | 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_6.srf | srf | 1150193272.0 | 7567061.0 | E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert | 0:76 1:76 | A:280621121;C:291623460;G:285422205;T:273609496;N:18916990 | 76 | 76 | 280621121 | 291623460 | 285422205 | 273609496 | 18916990 | ERX005931 | ERS000090 | ERA010603 | SC|Wellcome Trust Sanger Institute | SC|Wellcome Trust Sanger Institute | 2 | 0.96663 | 0.96605 | 0.0126 | 0.01249 | 0.82272 | 0.82548 | 0.45602 | 0.45286 | 76 | 76 | B | B | biological fallback assumption | illumina | early_illumina | 3prime | other | unknown | bulk | unknown | unknown | United Kingdom | 2010-02-26 | Adult | Adult | Gonad | Reproductive System |