{"database": "metadata", "table": "run_metadata", "rows": [[30567, "SRR27836082", "SRX23499413", "SRS20351171", "SRP487485", "PRJNA1072072", "Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios", "GSE254850", "Transcriptome Analysis", "Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.", null, "pubmed:38898112", null, "rbpms2 wildtype 3  21 dpf", "GSM8059031", null, "source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing", "rbpms2 wildtype 3  21 dpf", "Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample", "Gonad", null, "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype", "GSM8059031", "GSM8059031: rbpms2 wildtype 3  21 dpf; Danio rerio; RNA Seq", "GSM8059031 r1", "GSM8059031", "1", "RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487485", null, "loader:fastq load.py", "rbpms2-d21-WT_3_S3_L002_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L002_R2_001.fastq.gz", "fastq fastq", 2018915070.0, 19793285.0, "GSM8059031 r2", "0:51 1:51", "A:603776465;C:403221066;G:408169193;T:603728354;N:19992", 51, 51, null, null, 603776465, 403221066, 408169193, 603728354, 19992, "SRX23499413", "SRS20351171", "SRA1796363", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", "Marlow, CDRB, Icahn School of Medicine Mount Sinai", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-02-01", "Larval", "Larval", "Gonad", "Reproductive System"]], "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": ["30567"], "units": {}, "query_ms": 13.548795999668073}