run_metadata: 68633
This data as json
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| 68633 | SRR18054179 | SRX14206221 | SRS12028354 | 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. | Oocyte development Oocyte stage II 100 300μm 7/16/14 Biorep1 | Oocyte development Oocyte II B1 AGN001113 | strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000974|replicate ref:AGN001113|replicate order:1|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte II|replicate label short:Oocyte II B1|BioSampleModel:Model organism or animal | Oocyte development Oocyte stage II 100 300m 7/16/14 Biorep1 | AGR001537 | AGR001537 | mRNA | RNA-Seq | TRANSCRIPTOMIC | unspecified | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP360207 | AGR001537_R1.fastq.gz | fastq | 450099360.0 | 5922360.0 | AGR001537 R1.fastq.gz | 0:76 1:0 | A:117120225;C:103500083;G:101671751;T:121875501;N:5931800 | 76 | 0 | 117120225 | 103500083 | 101671751 | 121875501 | 5931800 | SRX14206221 | SRS12028354 | SRA1373868 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 1 | 0.96171 | 0.03386 | 0.75635 | 0.47167 | 76 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2022-02-21 | Zygote | Embryo | Embryo Imprecise | All anatomical structures |