{"database": "metadata", "table": "run_metadata", "rows": [[47629, "SRR6784679", "SRX3744217", "SRS3000686", "SRP133517", "PRJNA436017", "Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition", "GSE111152", "Transcriptome Analysis", "During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.", null, "pubmed:29625039", null, "Zebrafish 4 hpf whole embryo injected with TUT7MO Exp. ID: rs1a", "GSM3024071", null, "tissue:Zebrafish whole embryo|hpf translation blocking|strain:AB", "Zebrafish 4 hpf whole embryo injected with TUT7MO Exp. ID: rs1a", "The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The \"rs1a\" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have \u2265 256 \u201cexpected counts\u201d of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with \u2264 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.", "Zebrafish whole embryo", "Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5\u02daC. Embryos were staged according to standard morphological criteria.", "hpf translation blocking|strain:AB", "GSM3024071", "GSM3024071: Zebrafish 4 hpf whole embryo injected with TUT7MO Exp. ID: rs1a; Danio rerio; RNA Seq", "GSM3024071", null, "1", "For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.", "GEO Accession:GSM3024071", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP133517", null, null, "rs1a-TUT7MO-4hpf_R2.fastq.gz rs1a-TUT7MO-4hpf_R1.fastq.gz", "fastq fastq", 5768921100.0, 38459474.0, "GSM3024071 r1", "0:75 1:75", "A:1555172603;C:1327529056;G:1315409284;T:1567647314;N:3162843", 75, 75, null, null, 1555172603, 1327529056, 1315409284, 1567647314, 3162843, "SRX3744217", "SRS3000686", "SRA662359", "GEO", "Narry Kim Lab, Center for RNA Research, Institute for Basic Science", 2, 0.95735, 0.96309, 0.08315, 0.08265, 0.76493, 0.76806, 0.72767, 0.73332, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "bulk", "bulk", null, "South Korea", "2018-02-26", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"]], "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": ["47629"], "units": {}, "query_ms": 10.898612999881152}