run_metadata: 36277
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 |
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| 36277 | SRR298562 | SRX079840 | SRS212646 | SRP007331 | PRJNA141525 | Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. | GSE29418 | Transcriptome Analysis | RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform. | pubmed:21743441 | TDRD1IPlong | GSM727519 | tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL | TDRD1IPlong | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. | RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract | Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Tdrd1 antibody 1:100 in a total volume of 500 µl. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing. | strain:TL | GSM727519 | GSM727519: TDRD1IPlong | GSM727519: TDRD1IPlong | GSM727519: TDRD1IPlong | 1 | GEO Accession:GSM727519 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP007331 | read name barcode proc directive:ignore | TDRD1IPlong.fastq | fastq | 1098157770.0 | 23872995.0 | GSM727519 1 | 0:46 | 46 | SRX079840 | SRS212646 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.63282 | 0.29001 | 0.80095 | 0.51046 | 46 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Undetermined | Undetermined | Multi-tissue | Multi-system |