run_metadata: 33659
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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| 33659 | SRR30476759 | SRX25901727 | SRS22493412 | SRP529442 | PRJNA1154244 | ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [RNA Seq] | GSE275992 | Transcriptome Analysis | Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs 80 ribosomal proteins and over 200 biogenesis factors that take part in numerous interdependent steps. The complexity and essentiality of this process creates opportunities for deleterious mutations to occur accumulate and impact downstream cellular processes. “Dead end” ribosome intermediates that result from biogenesis errors are rapidly degraded affirming the existence of quality control pathways that monitor ribosome assembly. However the factors that differentiate between on path and dead end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway which we term the Ribosome Assembly Surveillance Pathway RASP. In an animal model loss of ZNF574 leads to developmental defects further emphasizing the importance of RASP in organismal health. Overall design: To identify differentially expressed genes following the loss of znf574 we in crossed znf574+/ animals. znf574 wild type znf574+/+ or +/ and znf574 mutant znf574 / larvae were phenotypically identified seven dpf Whole animals were used for this experiment. We performed RNA Seq followed by differential expression analysis with DESeq2 comparing differentially expressed genes between ZNF574 mutant and wild type animals. | pubmed:40328246 | Whole Body Mut R2 | GSM8489057 | tissue:whole larvae|cell line:whole larvae|cell type:all cell types|genotype:znf574 / |treatment:N1|time:NA|geo loc name:missing|collection date:missing | Whole Body Mut R2 | Reads were de multiplexed using Illumina’s bcl2fastq v2.20. Reads were aligned to the zebrafish genome GRCz11/danRer11 using kallisto v0.46.0. DESeq2 Galaxy Version 2.11.40+galaxy2 was used for differential expression analysis Genes with a minimum two fold upregulation in znf574 / larvae and an adjusted p value of less than 0.05 were selected for further analysis. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes database KEGG www.genome.jp/kegg. Pathway enrichment analyses were performed by using the Database for Annotation Visualization and Integrated Discovery DAVID Bioinformatics https://david.ncifcrf.gov/tools.jsp. Assembly: GRCz11/danRer11 Supplementary files format and content: tab separated value file that includes the raw count for each sample | whole larvae | znf574+/ heterozygous animals were in crossed and fertilized eggs were collected and maintained in a zebrafish incubator for 8 days. Water was exchanged daily. Seven dpf znf574 mutant animals can be easily distinguished from wild type siblings. | RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595. | Adult zebrafish were maintained on a 14 h light–10 h dark cycle and fed once daily with 3.5% body weight of Gemma Micro 500 Skretting USA. All genotypes were bred into the wild type AB background. All procedures comply with all relevant ethical regulations and were approved by the Carnegie Institution Animal Care and Use Committee Protocol #162 and the animal ethics committee IACUC review board at the Stowers Institute for MedicalResearch Protocol #2024 171. | cell line:whole larvae|cell type:all cell types|genotype:znf574 / |treatment:N1|time:NA | GSM8489057 | GSM8489057: Whole Body Mut R2; Danio rerio; RNA Seq | GSM8489057 r1 | GSM8489057 | 1 | RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP529442 | 6_Whole_Body_Mutant_S8_L004_R1_001.fastq.gz | fastq | 766293825.0 | 10217251.0 | GSM8489057 r1 | 0:75 | A:194461148;C:175434886;G:181181789;T:215200139;N:15863 | 75 | 194461148 | 175434886 | 181181789 | 215200139 | 15863 | SRX25901727 | SRS22493412 | SRA1958985 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | 1 | 0.96072 | 0.1396 | 0.66892 | 0.47985 | 75 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2024-08-29 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures |