{"database": "metadata", "table": "run_metadata", "rows": [[68606, "SRR18052577", "SRX14204750", "SRS12026894", "SRP360172", "PRJNA807674", "A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb", "PRJNA807674", "Other", "The Balbiani body Bb is the first marker of polarity in vertebrate oocytes. The Bb is a conserved structure found in diverse animals including insects  fish  amphibians  and mammals. During early zebrafish oogenesis  the Bb assembles as a transient aggregate of mRNA  proteins  and membrane bound organelles at the presumptive vegetal side of the oocyte. As the early oocyte develops  the Bb appears to grow slowly  until at the end of stage I of oogenesis it disassembles and deposits its cargo of localized mRNAs and proteins. In fish and frogs  this cargo includes the germ plasm as well as gene products required to specify dorsal tissues of the future embryo. We demonstrate that the Bb is a stable  solid structure that forms a size exclusion barrier similar to other biological hydrogels. Despite its central role in oocyte polarity  little is known about the mechanism behind the Bb's action. Analysis of the few known protein components of the Bb is insufficient to explain how the Bb assembles  translocates  and disassembles. We isolated Bbs from zebrafish oocytes and performed mass spectrometry to define the Bb proteome. We successfully identified 77 proteins associated with the Bb sample  including known Bb proteins and novel RNA binding proteins. In particular  we identified Cirbpa and Cirbpb  which have both an RNA binding domain and a predicted self aggregation domain. In stage I oocytes  Cirbpa and Cirbpb localize to the Bb rather than the nucleus as in somatic cells  indicating that they may have a specialized function in the germ line. Both the RNA binding domain and the self aggregation domain are sufficient to localize to the Bb  suggesting that Cirbpa and Cirbpb interact with more than just their mRNA targets within the Bb. We propose that Cirbp proteins crosslink mRNA cargo and proteinaceous components of the Bb as it grows. Beyond Cirbpa and Cirbpb  our proteomics dataset presents many candidates for further study  making it a valuable resource for building a comprehensive mechanism for Bb function at a protein level.", null, null, null, "Oocyte development   Oocyte stage 1.3 40 70\u03bcm 7/14/14 Biorep2", "Oocyte development   Oocyte I.3 B2 AGN001112", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000972|replicate ref:AGN001112|replicate order:2|project label long:Zebrafish oocyte development from Mullins Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte I.3|replicate label short:Oocyte I.3 B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage 1.3 40 70m 7/14/14 Biorep2", "AGR001536", "AGR001536", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360172", null, null, "AGR001536_R1.fastq.gz", "fastq", 467635448.0, 6153098.0, "AGR001536 R1.fastq.gz", "0:76 1:0", "A:123171986;C:108126001;G:105088073;T:125086357;N:6163031", 76, 0, null, null, 123171986, 108126001, 105088073, 125086357, 6163031, "SRX14204750", "SRS12026894", "SRA1373771", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96741, null, 0.02607, null, 0.7763, null, 0.49394, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "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": ["68606"], "units": {}, "query_ms": 7.921265001641586}