{"database": "metadata", "table": "run_metadata", "rows": [[34042, "SRR31033349", "SRX26418801", "SRS22938437", "SRP539223", "PRJNA1174207", "Rbm24 dictates mRNA recruitment for germ plasm assembly", "GSE279756", "Transcriptome Analysis", "Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.", null, null, null, "Zebrafish  RNAseq  M 24HPF 3", "GSM8579725", null, "source name:whole embryo|tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing", "Zebrafish  RNAseq  M 24HPF 3", "Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|Stage:24 hpf stage|cell type:embryonic cell|genotype:Mrbm24a", "GSM8579725", "GSM8579725: Zebrafish  RNAseq  M 24HPF 3; Danio rerio; RNA Seq", "GSM8579725 r1", "GSM8579725", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539223", null, null, "M-24HPF-3_L1_1.fq.gz M-24HPF-3_L1_2.fq.gz", "fastq fastq", 6652426200.0, 22174754.0, "GSM8579725 r1", "0:150 1:150", "A:1801675309;C:1524819778;G:1581222646;T:1744664175;N:44292", 150, 150, null, null, 1801675309, 1524819778, 1581222646, 1744664175, 44292, "SRX26418801", "SRS22938437", "SRA1993092", "Shandong university", "Shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-10-17", "Pharyngula", "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": ["34042"], "units": {}, "query_ms": 9.98060999882}