{"database": "metadata", "table": "run_metadata", "rows": [[68631, "SRR18054177", "SRX14206223", "SRS12028357", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage III >300\u03bcm 7/18/14 Biorep1", "Oocyte development   Oocyte III B1 AGN001117", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000976|replicate ref:AGN001117|replicate order:1|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte III|replicate label short:Oocyte III B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage III >300m 7/18/14 Biorep1", "AGR001529", "AGR001529", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001529_R1.fastq.gz", "fastq", 533176860.0, 7015485.0, "AGR001529 R1.fastq.gz", "0:76 1:0", "A:134362652;C:123935022;G:124704799;T:143147744;N:7026643", 76, 0, null, null, 134362652, 123935022, 124704799, 143147744, 7026643, "SRX14206223", "SRS12028357", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96834, null, 0.02909, null, 0.75666, null, 0.46022, 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": ["68631"], "units": {}, "query_ms": 7.854244991904125}