run_metadata: 62498
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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| 62498 | SRR13234614 | SRX9666712 | SRS7865649 | SRP297464 | PRJNA683902 | Ythdf m6A readers function redundantly during zebrafish development | PRJNA683902 | Other | During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability. | MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 6hpf triptolide polyA | MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 bkgd match WT 6h trip pA AGN001786 | strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |treatment:triptolide|molecule:mRNA|selection:pA|sample ref:AGS001432|replicate ref:AGN001786|replicate order:1|BioSampleModel:Model organism or animal | MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 6hpf triptolide polyA | AGR002446 | AGR002446 | mRNA | RNA-Seq | TRANSCRIPTOMIC | unspecified | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP297464 | AGR002446_R1.fastq.gz | fastq | 1124283808.0 | 14793208.0 | AGR002446 R1.fastq.gz | 0:76 1:0 | A:303085193;C:262065829;G:254422392;T:304661911;N:48483 | 76 | 0 | 303085193 | 262065829 | 254422392 | 304661911 | 48483 | SRX9666712 | SRS7865649 | SRA1169659 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 1 | 0.90758 | 0.10149 | 0.75298 | 0.50822 | 76 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-12-09 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures |