Ontology highlight
ABSTRACT:
PROVIDER: PRJNA576013 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10235856_1.fastq.gz | Fastqsanger.gz | |||
| SRR10235856_2.fastq.gz | Fastqsanger.gz | |||
| SRR10235857_1.fastq.gz | Fastqsanger.gz | |||
| SRR10235857_2.fastq.gz | Fastqsanger.gz | |||
| SRR10235858_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
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Project description:The extent to which mRNA and protein levels correlate is still not fully known, especially during development, when cells undergo a major transition in gene expression. One organism with particular development is Dictyostelium discoideum, during which it transitions from free-living unicellular to multicellular. Previously the transcriptome has been thoroughly studied during multicellular development, however the proteome and its correlation to the transcriptome during this transition is not fully understood.
In this study, for the first time, paired transcriptomics and proteomics was performed in a time series during aggregative multicellularity. From the analysis, the majority of transcripts were identified as differentially expressed, and we could quantify roughly a third of the proteome during early multicellular development. The proteome and transcriptome correlate relatively highly during steady-state, however this decreases as soon as multicellular aggregation is initiated. Correlation is particularly low at the gene-level during development. We find that dynamically regulated mRNA often leads to linear up- or downregulation of the protein, and that there is a time lag of approximately 2 to 4 hours between mRNA and protein.
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Project description:The Zebrafish transcriptome during early development
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Project description:Female fertility is determined in part by the size and development of the primordial follicle pool. The current study investigates the role of glial cell-line derived neurotrophic factor (GDNF) in the regulation of primordial follicle development in the ovary. Ovaries from four-day old female rat pups were maintained in organ culture for ten days in the absence (control) or presence of GDNF or kit ligand/stem cell factor (KL). Ovaries treated with GDNF contained a significant increase in developing follicles, similar to that observed with KL treatment previously shown to promote follicle development. The actions of GDNF on the ovarian transcriptome were investigated with a microarray analysis. Immunohistochemical studies demonstrated that GDNF is localized to oocyte cytoplasm in follicles of all developmental stages, as well as to cumulus granulosa cells and theca cells in antral follicles. GDNF receptor alpha 1 (GFRalpha1) staining was localized to oocyte cytoplasm of primordial and primary follicles, and at reduced levels in oocytes of antral follicles. GFRalpha1 was present in mural granulosa cells of antral follicles, theca cells, and the ovarian surface epithelium. The localization studies were confirmed with molecular analysis. Microarray analysis was used to identify changes in the ovarian transcriptome and further elucidate the signaling network regulating early follicle development. Observations indicate that GDNF promotes primordial follicle development and mediates autocrine and paracrine cell-cell interactions required during folliculogenesis. In contrast to the testis, ovarian GDNF is predominantly produced by germ cells (oocytes) rather than somatic cells. Experiment Overall Design: RNA samples from two control groups (pooled untreated cultured ovaries) are compared to two treated groups (pooled cultured ovaries treated with GDNF)
2008-06-11 | E-GEOD-11133 | biostudies-arrayexpress
Project description:Mammalian female reproductive lifespan is typically significantly shorter than life expectancy and is associated with a decrease in ovarian NAD levels. However, the mechanisms underlying this loss of ovarian NAD are unclear. Here, we show that CD38, a NAD consuming enzyme, is expressed in the ovarian extrafollicular space, primarily in immune cells, and its levels increase with reproductive age. Reproductively young mice lacking CD38 exhibit larger primordial follicle pools, elevated ovarian NAD levels, and increased fecundity relative to wild type controls. This larger ovarian reserve results from a prolonged window of follicle formation during early development. However, the beneficial effect of CD38 loss on reproductive function is not maintained at advanced age. Our results demonstrate a novel role of CD38 in regulating ovarian NAD metabolism and establishing the ovarian reserve, a critical process that dictates a female reproductive lifespan.
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Project description:Female fertility is determined in part by the size and development of the primordial follicle pool. The current study investigates the role of glial cell-line derived neurotrophic factor (GDNF) in the regulation of primordial follicle development in the ovary. Ovaries from four-day old female rat pups were maintained in organ culture for ten days in the absence (control) or presence of GDNF or kit ligand/stem cell factor (KL). Ovaries treated with GDNF contained a significant increase in developing follicles, similar to that observed with KL treatment previously shown to promote follicle development. The actions of GDNF on the ovarian transcriptome were investigated with a microarray analysis. Immunohistochemical studies demonstrated that GDNF is localized to oocyte cytoplasm in follicles of all developmental stages, as well as to cumulus granulosa cells and theca cells in antral follicles. GDNF receptor alpha 1 (GFRalpha1) staining was localized to oocyte cytoplasm of primordial and primary follicles, and at reduced levels in oocytes of antral follicles. GFRalpha1 was present in mural granulosa cells of antral follicles, theca cells, and the ovarian surface epithelium. The localization studies were confirmed with molecular analysis. Microarray analysis was used to identify changes in the ovarian transcriptome and further elucidate the signaling network regulating early follicle development. Observations indicate that GDNF promotes primordial follicle development and mediates autocrine and paracrine cell-cell interactions required during folliculogenesis. In contrast to the testis, ovarian GDNF is predominantly produced by germ cells (oocytes) rather than somatic cells. Keywords: expression analysis, glial derived neurotrophic factor, follicle transition, ovary
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Project description:Mammalian female reproductive lifespan is typically significantly shorter than life expectancy and is associated with a decrease in ovarian NAD levels. However, the mechanisms underlying this loss of ovarian NAD are unclear. Here, we show that CD38, a NAD consuming enzyme, is expressed in the ovarian extrafollicular space, primarily in immune cells, and its levels increase with reproductive age. Reproductively young mice lacking CD38 exhibit larger primordial follicle pools, elevated ovarian NAD levels, and increased fecundity relative to wild type controls. This larger ovarian reserve results from a prolonged window of follicle formation during early development. However, the beneficial effect of CD38 loss on reproductive function is not maintained at advanced age. Our results demonstrate a novel role of CD38 in regulating ovarian NAD metabolism and establishing the ovarian reserve, a critical process that dictates a female reproductive lifespan.
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Project description:The Homeobox (HOX) family of genes encodes transcription factors involved in basic developmental processes, most notably during embryogenesis. A possible HOX gene link between development and oncogenesis has recently been described. Dysregulation of HOX genes may be an early event in malignant transformation likely to induce antibody response and thus provide a potential marker for early diagnosis of cancer. Ovarian cancer is characterized by poor early detection and serves as an excellent model system to develop potential markers for early diagnosis. In this study we begin to characterize HOX gene expression in malignant tumors of the ovary and analyze the potential role of HOX genes as biomarkers for early detection of ovarian cancer. Microarray analysis of mRNA from human ovarian tissues was performed on 65 samples of normal, benign, borderline malignant and malignant ovarian tissue. These samples were analyzed using the Affymetrix Human Genome Focus GeneChip (HG-Focus) microarray to distinguish the differential pattern of mRNA expression between the four types of samples. Real-time reverse transcription PCR was utilized to confirm up-regulation of HOX genes as determined by microarray analysis. Our results demonstrate multiple HOX genes to be up-regulated in ovarian cancer. We have shown stepped increase in HOX expression comparing normal, benign neoplastic, and malignant human ovarian tissue samples. This suggests dysregulation of HOX genes may be an early event in malignant transformation and warrants additional studies to validate HOX gene products as potential markers for early detection of ovarian cancer. Experiment Overall Design: 67 samples were analyzed. 4 groupings based on pathology (normal, benign, borderline malignant, malignant). An average of normal samples was used as controls. Cell lines were used as ovarian cancer control samples.
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