run_metadata: 31690
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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| 31690 | SRR28490628 | SRX24092860 | SRS20882181 | SRP498456 | PRJNA1093028 | Effect of depletion of Sas10 in pre rRNA processing | GSE262698 | Transcriptome Analysis | Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples. | pubmed:39036955 | zebrafish embryo 5dpf wild type rep 1 | GSM8173999 | source name:embryo|tissue:embryo|genotype:wild type|geo loc name:missing|collection date:missing | zebrafish embryo 5dpf wild type rep 1 | Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size. | embryo | Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs. | tissue:embryo|genotype:wild type | GSM8173999 | GSM8173999: zebrafish embryo 5dpf wild type rep 1; Danio rerio; RNA Seq | GSM8173999 r1 | GSM8173999 | 1 | Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs. | RNA-Seq | TRANSCRIPTOMIC | RACE | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP498456 | RACE_AB_1_R2.fq.gz RACE_AB_1_R1.fq.gz | fastq fastq | 4575871800.0 | 15252906.0 | GSM8173999 r1 | 0:150 1:150 | A:718107616;C:1095325729;G:1919360747;T:842938887;N:138821 | 150 | 150 | 718107616 | 1095325729 | 1919360747 | 842938887 | 138821 | SRX24092860 | SRS20882181 | SRA1835384 | MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University | MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University | 2 | 0.14402 | 0.00584 | 0.14352 | 0.00565 | 0.99935 | 0.99955 | 0.60273 | 0.77777 | 150 | 150 | B | T | mate2 technical by mapping diff | illumina | novaseq_era | 3prime | other | unknown | bulk | unknown | unknown | China | 2024-03-28 | Larval | Larval | Embryo Imprecise | All anatomical structures |