run_metadata: 30730
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 30730 | SRR28342053 | SRX23948600 | SRS20750289 | 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 upf1 RESA HITS CLIP B5 | 3xflag upf1 RESA HITS CLIP B5 AGN003270 | strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|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:AGS002505|replicate ref:AGN003270|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 IP|replicate label short:RESA CLIP Upf1 #3650 IP B2|BioSampleModel:Model organism or animal | 3xflag upf1 RESA HITS CLIP B5 | AGR004050 | AGR004050 | PCR from library specific RT | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP495203 | AGR004050_R1.fastq AGR004050_R2.fastq | fastq fastq | 11823214534.0 | 39149717.0 | AGR004050 R1.fastq.zst | 0:151 1:151 | A:3184473505;C:2558650081;G:3236214151;T:2843828317;N:48480 | 151 | 151 | 3184473505 | 2558650081 | 3236214151 | 2843828317 | 48480 | SRX23948600 | SRS20750289 | 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 |