run_metadata: 41459
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41459 | SRR4449276 | SRX2267732 | SRS1758936 | SRP092030 | PRJNA350377 | Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly | PRJNA350377 | Transcriptome Analysis | Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly | Danio rerio embryo at approx. 50% epiboly | Danio rerio embryo at approx. 50% epiboly | S07 RID0445 | strain:ABTL|dev stage:47% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal | S07 | S07 RID0445 | S07 RID0445 | Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific. | miRNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP092030 | IonXpressRNA_007_rawlib.basecaller.bam | bam | 50356775.0 | 1885340.0 | IonXpressRNA 007 rawlib.basecaller.bam | 0:26.71 | A:13603929;C:11508700;G:12096780;T:13147366;N:0 | 26 | 13603929 | 11508700 | 12096780 | 13147366 | 0 | SRX2267732 | SRS1758936 | SRA486759 | UNIVERSITY OF AMSTERDAM, SILS|RB&AB | UNIVERSITY OF AMSTERDAM, SILS | 1 | 0.63582 | 0.39586 | 0.79839 | 0.56846 | 22 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | small_rna | unknown | bulk | unknown | unknown | Netherlands | 2017-11-01 | Gastrula | Embryo | Whole Organism | All anatomical structures |