{"database": "metadata", "table": "run_metadata", "rows": [[34616, "SRR32137215", "SRX27483375", "SRS23906279", "SRP560121", "PRJNA1216205", "rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation", "GSE288109", "Other", "The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish  we performed RIP seq analysis using rbm24a GFP knock in samples  with IgG serving as the control.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in2 IgG2", "GSM8759067", null, "source name:whole embryo|tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in|geo loc name:missing|collection date:missing", "Zebrafish  RIP seq  Rbm24a Knock in2 IgG2", "Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample", "whole embryo", null, "Total RNAs were extracted from 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94\u00b0C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2\u00d7150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in", "GSM8759067", "GSM8759067: Zebrafish  RIP seq  Rbm24a Knock in2 IgG2; Danio rerio; RIP Seq", "GSM8759067 r1", "GSM8759067", "1", "Total RNAs were extracted from 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94\u00b0C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2\u00d7150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP560121", null, null, "RIP_IgG2.R1.fq.gz RIP_IgG2.R2.fq.gz", "fastq fastq", 18588838088.0, 61552444.0, "GSM8759067 r1", "0:151 1:151", "A:3864885070;C:5250483318;G:5713729791;T:3756127723;N:3612186", 151, 151, null, null, 3864885070, 5250483318, 5713729791, 3756127723, 3612186, "SRX27483375", "SRS23906279", "SRA2061743", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-27", "Multi-stage", "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": ["34616"], "units": {}, "query_ms": 8.258098998339847}