run_metadata: 36271
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36271 | SRR298568 | SRX079846 | SRS212652 | 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 | ZiwiIPTes | GSM727525 | tissue:RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract|strain:TL | ZiwiIPTes | 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 Ziwi 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 Ziwi antibody in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. 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 | GSM727525 | GSM727525: ZiwiIPTes | GSM727525: ZiwiIPTes | GSM727525: ZiwiIPTes | 1 | GEO Accession:GSM727525 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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 | ZiwiIPTes.fastq | fastq | 976120596.0 | 27114461.0 | GSM727525 1 | 0:36 | 36 | SRX079846 | SRS212652 | SRA039167 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.10415 | 0.03658 | 0.96173 | 0.30033 | 36 | B | usable mapping rate | illumina | early_illumina | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Netherlands | 2011-05-20 | Undetermined | Undetermined | Multi-tissue | Multi-system |