run_metadata: 76560
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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| 76560 | SRR25071780 | SRX20825792 | SRS18104431 | SRP446536 | PRJNA989133 | Translation of zinc finger domains induces ribosome collision and Znf598 dependent mRNA decay in zebrafish [RNA seq] | GSE236143 | Transcriptome Analysis | Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes triggering ribosome associated quality control RQC to rescue stalled ribosomes and no go decay NGD to degrade stall prone mRNAs. However the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study we investigated the endogenous substrate mRNAs of NGD during the maternal to zygotic transition MZT of zebrafish development. RNA Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 downregulates mRNAs encoding the C2H2 type zinc finger domain C2H2 ZF during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2 ZFs leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2 ZF sequences in the vertebrate genome. Overall design: RNA seq | parent bioproject:PRJNA989127 | pubmed:39636823 | Wild type 1 hpf rep1 | GSM7518805 | source name:Whole embryo|tissue:Whole embryo|genotype:Wild type AB strain|geo loc name:missing|collection date:missing | Wild type 1 hpf rep1 | Basecalling with Illumina Casava 1.8 software Analyzed using Galaxy on public server three prime adapter trimming with Fastp Alignment to genome with STAR v2.7.8a with outFilterMismatchNmax 1 outFilterMultimapNmax 1 options Read quantitation using featureCounts v3.36.0 Assembly: GRCz11 Supplementary files format and content: text files tab separated values contain two columns: 1. gene id; 2. read counts | Whole embryo | Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina | Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC. | tissue:Whole embryo|genotype:Wild type AB strain | GSM7518805 | GSM7518805: Wild type 1 hpf rep1; Danio rerio; RNA Seq | GSM7518805 r1 | GSM7518805 | 1 | Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP446536 | AB_1h-1.fastq.gz | fastq | 1692730103.0 | 22429081.0 | GSM7518805 r1 | 0:75.47 | A:387190897;C:441464631;G:408597629;T:455327744;N:149202 | 75 | 387190897 | 441464631 | 408597629 | 455327744 | 149202 | SRX20825792 | SRS18104431 | SRA1664576 | Department of Frontier Life Sciences, Kyoto Sangyo University | Department of Frontier Life Sciences, Kyoto Sangyo University | 1 | 0.91584 | 0.06124 | 0.75041 | 0.54867 | 76 | B | usable mapping rate | illumina | nextseq | unknown | rrna_depletion | ribozero | bulk | bulk | bulk | Japan | 2023-06-29 | Cleavage | Embryo | Whole Organism | All anatomical structures |