Transcriptomics of granulosa cells(GCs) from healthy follicles(HFs), early atretic follicles(EFs) and late atretic follicle(LFs) in Chinese buffalo
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ABSTRACT:
PROVIDER: PRJNA713391 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13931407_1.fastq.gz | Fastqsanger.gz | |||
| SRR13931407_2.fastq.gz | Fastqsanger.gz | |||
| SRR13931408_1.fastq.gz | Fastqsanger.gz | |||
| SRR13931408_2.fastq.gz | Fastqsanger.gz | |||
| SRR13931409_1.fastq.gz | Fastqsanger.gz |
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Project description:GCs were collected from HFs and AFs , to use second-generation high-throughput sequencing for whole-transcriptome analysis, respectively. In total, 1861 and 1075 mRNAs, 159 and 24 miRNAs, 123 and 100 lncRNAs, and 58 and 54 circRNAs were identified to be differentially expressed (DE) in up-regulated and down-regulated. Enrichment of functions and signaling pathways of the DEgenes showed that most of DEmRNAs and targets of DEmiRNAs, DElncRNAs and DEcricRNAs were annotated to the categories of ‘PI3K-Akt signaling pathway’, ‘ECM-receptor interaction’, ‘Focal adhesion’, ‘mTOR signaling pathway ’ ‘TGF-beta signaling pathway’, ‘Rap1 signaling pathway’, and ‘Estrogen signaling pathway’. The ceRNA (competing endogenous RNA) network was constructed based on ceRNA theory further revealed regulatory roles of these DERNAs in granulosa cells of buffalo atretic follicles. A large number of mRNAs, lncRNAs, circRNAs, and miRNAs in buffalo granulosa were altered in healthy and atretic follicles, which may play crucial roles in atretic of buffalo follicles through the ceRNA regulatory network.
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Project description:Compared with granulosa cells from healthy follicles, 2888 (1790 up-regulated, 1098 down-regulated) and 1629 (1230 up-regulated, 399 down-regulated) DEGs (|FC| > 1.75 and P value < 0.05) were identified in granulosa cells of early atretic follicles and late atretic follicle, respectively. Out of these DEGs, 1217 genes were commonly shared among the two comparisons
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Project description:Granulosa cells originating from two different phases of antral follicle growth (plateau and atretic) were compared in follicles with a diameter of 9mm or more. The plateau follicle is the reference. Two conditions experiment (Plateau and Atretic); Four biological replicates for each group; Two technical replicates per samples (dye-swap).
2015-03-06 | E-GEOD-63919 | biostudies-arrayexpress
Project description:Granulosa cells originating from two different phases of antral follicle growth (plateau and atretic) were compared in follicles with a diameter of 9mm or more. The plateau follicle is the reference.
2015-03-06 | GSE63919 | GEO
Project description:Granulosa cells mature and die as ovarian follicles enlarge and die (undergo atresia) under the influence of hormones and intrafollicular factors. Later in follicular development, a fluid-filled antrum is formed, a process which is accompanied by a high rate of atresia. These small antral follicles (5 mm or less in diameter in the cow) contain granulosa of 2 different phenotypes, rounded or columnar, whereas follicles larger than 5 mm have the rounded phenotype only. Prior to ovulation, in larger follicles greater than 10 mm in size, the granulosa begin to migrate and differentiate in preparation for oocyte release and formation of the corpus luteum. These two key phases of follicular development were studied by gene expression microarray analysis using a bovine model to dissect the molecular mechanisms underlying these processes. Four groups of bovine ovarian follicles were selected for analysis. Follicle size, type and array number for each group are as follows: small (3-5 mm) healthy rounded (n=5), small healthy columnar (n=5), atretic (n=5) and large healthy (>10 mm; n=4). For each group, the RNA from a single follicle was used to hybridise an array, except for 3 small healthy samples which were pooled from 2 follicles each due to low RNA.
2014-05-20 | E-GEOD-39589 | biostudies-arrayexpress
Project description:Granulosa cells originating from three different phases of antral follicle growth were compared: growing (G), plateau (P) and atresia (A), as categorized by flow cytometry profiles of DNA. The growing and atretic conditions were each hybridized against the plateau condition as a reference in order to understand the specific biological mechanisms modulated in this class of follicles. Three-condition experiment, Plateau, Growing vs Atretic granulosa cells. Biological replicates: 4 . Dye-swap experiment.
2014-06-02 | E-GEOD-56145 | biostudies-arrayexpress
Project description:Cumulus cells (CCs) and mural granulosa cells (MGCs) have different phenotypes and different roles in the follicle. However, our previous reports have suggested that CCs and MGCs from bovine early antral follicles become MGC-like cells and CC-like cells, respectively. In this study, we examined whether granulosa cells (GCs) from secondary follicles and MGCs from late antral follicles were able to reconstruct complexes with transzonal projection (TZP)-free denuded oocytes (DOs) and regenerate TZPs similar to MGCs from early antral follicles. Furthermore, to confirm that the regenerated TZPs were functional, the development of reconstructed complexes and oocyte growth in the complexes were determined. After coculture, GCs were able to reconstruct complexes with DOs and regenerate TZPs similar to MGCs from early antral follicles. In addition, the oocytes in integrally reconstructed complexes grew fully and acquired meiotic competence, suggesting that the regenerated TZPs are functional. In contrast, MGCs from late antral follicles had lost the ability to elongate TZPs. Since the ability to regenerate TZPs differed among the cells, the transcriptome was analyzed among GCs, CCs, and MGCs collected from follicles of different sizes. The characteristic of TZP generation coincided with transcriptome changes in two directions from GCs to CCs and MGCs. In conclusion, until the early antral follicle stage, bovine GCs, CCs, and MGCs have common characteristics to elongate TZPs and form antrum-like structures to support oocyte growth in vitro. Furthermore, as the follicle develops, MGCs lose the ability to elongate TZPs.
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Project description:Granulosa cells originating from three different phases of antral follicle growth were compared: growing (G), plateau (P) and atresia (A), as categorized by flow cytometry profiles of DNA. The growing and atretic conditions were each hybridized against the plateau condition as a reference in order to understand the specific biological mechanisms modulated in this class of follicles.
2014-06-02 | GSE56145 | GEO
Project description:Human ovarian folliculogenesis is an highly regulated and complex process. Characterization of follicular cell signatures during this dynamic process is important to understand follicle fate (to grow, become dominant or undergo atresia). The transcriptional signature of human oocytes and granulosa cells (GC) in early-growing and ovulatory follicles have been previously described, however that of oocytes with surrounding GCs in small antral follicles have not been studied yet. Here, we have generated a unique dataset of single-cell transcriptomics (SmartSeq2) consisting of the oocyte with surrounding GCs from several individual (non-dominant) small antral follicles isolated from adult human ovaries. We have identified two main types of (healthy) follicles, with a distinct oocyte and GC signature. Using the CellphoneDB algorithm, we then investigated the bi-directional ligand-receptor interactions regarding the TGFβ/BMP, WNT, NOTCH, and receptor tyrosine kinases (RTK) signaling pathways between oocyte and GCs within each antral follicle type. Our work not only revealed the diversity of small antral follicles but also contributes to fill the gap in mapping the molecular landscape of human folliculogenesis and oogenesis.
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Project description:Antral follicle size might be a valuable additive predictive marker for IVF outcome. However, while some studies show positive relations between follicle size and reproductive outcome, others have not been successful in establishing this relation. To better understand consequences of antral follicle size for reproductive outcome, we aimed to obtain insight in follicle size-related granulosa cell processes, as granulosa cells play an essential role in follicular development via the production of growth factors, steroids and metabolic intermediates, needed for follicular growth and oocyte development. Using pigs as a model, we compared gene and protein expression in granulosa cells of smaller and larger follicles in the healthy antral follicle pool at the start of the follicular phase of the estrous cycle. In sows, the early antral follicle pool is very heterogeneous when e.g. size and steroid content of the follicular fluid are considered. To which extent this variety contributes to the developmental competence of the follicles is not clear. Therefore, sows with high variation in antral follicle size (HighVAR) as well as sows with low variation in antral follicle size (LowVAR) were used. Granulosa cells of smaller antral follicles in the healthy antral follicle pool show increased cell proliferation, which was accompanied by a metabolic shift towards aerobic glycolysis (i.e. the Warburg effect), similar to other highly proliferating cells. High granulosa cell proliferation rates in smaller follicles might be regulated via increased granulosa cell expression of AR and EGFR which are activated in response to locally produced mitogens. While granulosa cells of smaller follicles in the pool were more proliferative, indicative of higher follicular growth, granulosa cells of larger follicles in the pool showed less proliferation and were more differentiated, as they showed a higher expression of follicular maturation marker IGF1 and ANGPT1. Our results imply that the inclusion of strict criteria of antral follicle size in IVF protocols might improve reproductive outcome. In addition, we have granulosa cell gene expression of healthy follicles to unravel underlying mechanisms of differences in COC morphology. We compared gene expression in sows with low vs. high-COC-health and found a decreased expression of genes involved in ovarian steroidogenesis (e.g. CYP19A1, ADM, SPP1) and higher expression of genes involved in follicular atresia (e.g. GADD45A, INHBB) in sows with low-COC-health. Thereby we have identified several genes which may serve as markers for follicle developmental competence.
2019-08-15 | GSE125189 | GEO