{"database": "metadata", "table": "run_metadata", "rows": [[52265, "SRR9070359", "SRX5846427", "SRS4772045", "SRP198646", "PRJNA543299", "Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance zfRNAseq", "GSE131333", "Transcriptome Analysis", "RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We find disrupted nuclear RNA surveillance is oncogenic. Cyclin Dependent Kinase 13 CDK13 is mutated in melanoma and patient mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation  which is necessary and sufficient to promote nuclear RNA degradation. Mutant CDK13 fails to activate nuclear RNA surveillance  causing aberrant protein coding transcripts to be stabilized and translated. Forced aberrant RNA expression accelerates melanoma in zebrafish. We find recurrent mutations in genes encoding nuclear RNA surveillance components in many malignancies  establishing nuclear RNA surveillance as a tumor suppressive pathway. Activating nuclear RNA surveillance is crucial to avoid accumulation of aberrant RNAs and their ensuing consequences in development and disease. Overall design: RNA Seq in zebrafish melanoma expressing EGFP or mutant CDK13", "parent bioproject:PRJNA543289", null, null, "CDK13 R860Q oe R160", "GSM3770596", null, "source name:Melanoma|tissue:Melanoma|cdk13 status:R860Q", "CDK13 R860Q oe R160", "Reads were aligned to a custom version of the danRer10 genome that also contained the human CDK13 gene sequence using bowtie with parameters   library type fr unstranded   no novel juncs and  G set revision 90 of the Ensembl GRCz10 genes Expression of revision 90 GRCz10 genes was quantified using htseq count with parameters  r name  I gene name   stranded=no  m intersection strict Supplementary files format and content: Counts files contain gene names and htseq determined read counts", "Melanoma", null, "Library prepped with random priming NEBNext Ultra RNA Library Prep Kit for Illumina  E7530  fragmentation time of 15min  12 PCR cycles  and sequenced on an Illumina HiSeq 2000 100bp paired end reads. Melanomas were homogenized in RLT buffer  subjected to QIAshredder columns Qiagen  79656  and then RNA was isolated with a column based method with genomic DNA column removal Qiagen  74134.  RNA was ribodepleted Illumina Ribozero Gold  MRZG12324.  Ribodepletion was confirmed with Agilent 4200 Tapestation.", "p53 / ; mitfa:BRAFV600E;Na /  one cell embryos were injected with either 20ng/uL control or experimental MiniCoopR MCR DNA along with tol2 in vitro transcribed RNA for integration. In all experiments  20 zebrafish were raised per tank to control for density effects.  Zebrafish were scored for the emergence of raised melanoma lesions as published.  Zebrafish were sacrificed on ice and the tumors were dissected.", "tissue:Melanoma|cdk13 status:R860Q", "GSM3770596", "GSM3770596: CDK13 R860Q oe R160; Danio rerio; RNA Seq", "GSM3770596", null, "1", "Library prepped with random priming NEBNext Ultra RNA Library Prep Kit for Illumina  E7530  fragmentation time of 15min  12 PCR cycles  and sequenced on an Illumina HiSeq 2000 100bp paired end reads. Melanomas were homogenized in RLT buffer  subjected to QIAshredder columns Qiagen  79656  and then RNA was isolated with a column based method with genomic DNA column removal Qiagen  74134.  RNA was ribodepleted Illumina Ribozero Gold  MRZG12324.  Ribodepletion was confirmed with Agilent 4200 Tapestation.", "GEO Accession:GSM3770596", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP198646", null, null, "CDK13_R860Q_oe_R160.L001_R1.fastq.gz CDK13_R860Q_oe_R160.L001_R2.fastq.gz", "fastq fastq", 2678770600.0, 13393853.0, "GSM3770596 r1", "0:100 1:100", "A:619003093;C:719249623;G:727338824;T:611848801;N:1330259", 100, 100, null, null, 619003093, 719249623, 727338824, 611848801, 1330259, "SRX5846427", "SRS4772045", "SRA887503", "GEO", "Young Lab, Whitehead Institute for Biomedical Research", 2, 0.94125, 0.94048, 0.19284, 0.20048, 0.79644, 0.80397, 0.62455, 0.62265, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2019-05-16", "Undetermined", "Embryo", "Cancer or Tumor", "Cancer or Tumor"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["52265"], "units": {}, "query_ms": 10.792984001454897}