{"database": "metadata", "table": "run_metadata", "rows": [[63732, "SRR13998080", "SRX10375446", "SRS8490052", "SRP311218", "PRJNA715461", "RIP seq for Ddx3xb in zebrafish embryos", "GSE169161", "Other", "We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs  and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation  further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb  but not the Ddx3xb without xxx ability. Mechanistically  the condensation of Ddx3xb is vital for its RNA helicase activity  which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT  highlighting the critical role of protein phase separation in translational control and animal early development.    Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates", "parent bioproject:PRJNA715459", "pubmed:35661831", null, "rip 2h WT rep2", "GSM5179332", null, "source name:control 2h RIP seq rep2|tissue:zebrafish embryos|genotype:wild type|age:2 hpf", "rip 2h WT rep2", "low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options \u2018\u2013nomodel\u2019   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 \u00d7 10\u22122 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein", "control 2h RIP seq rep2", null, "flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4. Ddx3xb RIP was carried out following a published protocol  but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech  635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.", null, "tissue:zebrafish embryos|genotype:wild type|age:2 hpf", "GSM5179332", "GSM5179332: rip 2h WT rep2; Danio rerio; RIP Seq", "GSM5179332", null, "1", "RIP was carried out as previously described Despic et al.  2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc", "GEO Accession:GSM5179332", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311218", null, "loader:fastq load.py", "rip_2h_WT2.fq.gz", "fastq", 12320805000.0, 82138700.0, "GSM5179332 r1", "0:150", "A:3686415626;C:2826613772;G:3732955088;T:2073945227;N:875287", 150, null, null, null, 3686415626, 2826613772, 3732955088, 2073945227, 875287, "SRX10375446", "SRS8490052", "SRA1207702", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.1848, null, 0.11194, null, 0.9669, null, 0.82171, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2021-03-18", "Cleavage", "Embryo", "Embryo Imprecise", "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": ["63732"], "units": {}, "query_ms": 7.994380001036916}