{"database": "metadata", "table": "run_metadata", "rows": [[49535, "SRR7942606", "SRX4776871", "SRS3857410", "SRP162874", "PRJNA493827", "Transcriptomics analysis of gene expression in wide type  ybx1 MO  pabpc1a MO zebrafish embryo sample.", "GSE120643", "Other", "The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of [1] gene expressive levels in wide type and ybx1 MO zebrafish embryo [2] gene expressive levels in pabpc1a MO zebrafish embryo [3] mRNA lifetime in wide type zebrafish embryo. Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol Reagent Ambion. mRNA was extracted with using Dynabeads mRNA Purification Kit Ambion and subjected to TURBO DNase Invitrogen treatment at 37C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. Synchronously developing embryos were treated with 0.2 ng of Pol II inhibition alpha amanitin Sigma at one cell stage and were collected at indicated time points. 100 embryos were collected for each time point in duplicates. The total RNA was extracted by Trizol Invitrogen and used for RNA Seq. An equal amount of external RNA control consortium ERCC RNA spike in control Thermo Fisher was added to the total RNA samples as internal controls. The RNA was subjected to ribosomal RNA depletion with Ribo Zero rRNA Removal Kit Illumina followed by library construction using NEB Next\u00ae Ultra? RNA library Prep Kit NEB. RNA stability profiling was generated from two biological replicates.", "parent bioproject:PRJNA534030", null, null, "WT 0hpf rep2", "GSM3406870", null, "source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:0 hpf|tissue:whole embryo", "WT 0hpf rep2", "Reads were aligned to the zv9 genome assembly using TopHat v2.1.1 The number of reads mapped to each Ensemble gene was counted using the HTSeq v0.6.0 Genome build: zv9 Supplementary files format and content: Reads count for each gene in wild type  ybx1 MO and pabpc1a MO sample", "Zebrafish embryo", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", null, "strain:AB strain|cell type:Zebrafish embryo|age:0 hpf|tissue:whole embryo", "GSM3406870", "GSM3406870: WT 0hpf rep2; Danio rerio; RNA Seq", "GSM3406870", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "GEO Accession:GSM3406870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162874", null, "loader:latf load", "WT_0hpf_rep2_R1.fastq.gz WT_0hpf_rep2_R2.fastq.gz", "fastq fastq", 9235008100.0, 34013490.0, "GSM3406870 r1", "0:135.76 1:135.76", "A:2585376157;C:2035534424;G:2087400121;T:2523389569;N:3307829", 135, 135, null, null, 2585376157, 2035534424, 2087400121, 2523389569, 3307829, "SRX4776871", "SRS3857410", "SRA786936", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.95881, 0.96263, 0.02093, 0.01978, 0.79121, 0.79446, 0.71203, 0.33092, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-09-28", "Zygote", "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": ["49535"], "units": {}, "query_ms": 10.46808400133159}