run_metadata: 30725
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 30725 | SRR28342047 | SRX23948606 | SRS20750296 | SRP495203 | PRJNA1087701 | UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. | PRJNA1087701 | Other | Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD. | 3xflag upf3b RESA HITS CLIP B1 | 3xflag upf3b RESA HITS CLIP B1 AGN002795 | strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002161|replicate ref:AGN002795|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3b pulldown|replicate label short:Upf3b pulldown B1|BioSampleModel:Model organism or animal | 3xflag upf3b RESA HITS CLIP B1 | AGR003549 | AGR003549 | PCR from library specific RT | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP495203 | AGR003549_R1.fastq AGR003549_R2.fastq | fastq fastq | 9617196770.0 | 47609885.0 | AGR003549 R1.fastq.zst | 0:101 1:101 | A:2856263963;C:1963091501;G:2218118010;T:2579364306;N:358990 | 101 | 101 | 2856263963 | 1963091501 | 2218118010 | 2579364306 | 358990 | SRX23948606 | SRS20750296 | SRA1824033 | Yale University|Genetics | Yale University | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2024-03-14 | Blastula | Embryo | Embryo Imprecise | All anatomical structures |