Human oocyte DNA methylome
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE71985 | GEO | 2017/06/23
SECONDARY ACCESSION(S): PRJNA292685
REPOSITORIES: GEO
Similar Datasets
Project description:The goals of this study are to compare genome-wide DNA methylation levels in young and aged oocytes,and to investigate the transgenerational inheritance of methylome profiles in oocytes during natural aging. We apply a novel protocol of rapamycin to overcome the DNA methylation drift associated with oocyte aging. 8-week-old female mice were injected intraperitoneally with rapamycin or vehicle for 40 weeks. At the end of the experiment, females (48 weeks, F0) were paired with young adult (~4 mo old) males to produce F1 offspring (OF1 and ORaF1). An F2 generation (OF2 and ORaF2) resulted from mating F1 female at 44~48 weeks of age with young adult males. To generate YF1 and YF2 as normal control (offspring of young mother), we mated females (~8 weeks) with young adult males. Then we collect oocytes (F0,F1 and F2 generations)，sperm ( F1 and F2 generations) and hippocampus (F1 female offspring) from different groups to investigate the transgenerational inheritance of DNA methylome profiles associated with oocyte aging by the single cell whole-genome methylation sequencing (sc-WGBS). We found that oocytes from aged mother exhibited increased DNA methylation levels in CpG sites. Maternal aging related methylome changes can be inherited transgenerationally though oocyte to the germ line of F1 and F2 offspring. The application of rapamycin during the course of oocyte aging could reverse these DNA methylation alterations, and it can ameliorate several neurobehavioral aging trails that were in observed in aged oocyte offspring. WGBS-seq on DNA from hippocampal tissue revealed a number of differentially methylated (P<0.05) genes in OF1 and ORaF1 compared with YF1, and some of the enriched pathways were associated with aging process, such as PI3K-Akt signaling pathway (akin to transcriptional alterations above), MAPK signaling and Ras signaling pathway .
2022-12-31 | GSE164139 | GEO
Project description:The transition from a transcriptionally active state (GV) to a transcriptionally inactive state (mature MII oocytes) is one of the requirements for the acquisition of oocyte developmental competence. After maturation, oocytes are mostly transcriptionally quiescent, and developmental competence prior to embryonic genome activation (EGA) relies on maternal RNA and proteins. The landscape of expressed genes at the MII stage could be mostly driven by post-transcriptional mechanisms, such as alternative splicing (AS). With the development of single cell transcriptome analysis, genome wide AS analysis becomes technically feasible and available to fully characterize the AS patterns in human oocytes. Profiling spliced mRNA isoforms might provide novel information on the molecular mechanisms driving early development, and might be a source of potential biomarkers of oocyte quality. The goal of the present study is to perform a transcriptomic analysis in oocytes at different stages of maturation, to identify the profiles of alternative spliced isoforms produced in both oocyte’ stages.
2020-06-16 | GSE152525 | GEO
Project description:Somatic cells surrounding the oocyte were sampled at the following stages: developmentally incompetent or poorly competent prophase I oocytes (NC1 oocytes), developmentally competent prophase I oocytes (C1 oocytes), and developmentally competent metaphase II oocytes (C2 oocytes). NC1 samples were collected from late vitellogenic females (LV), C1 samples from post-vitellogenic females (PV), and C2 samples from females undergoing meiotic maturation (Germinal Vesicle Breakdown) Global transcriptional profiling was performed using somatic cells collected from rainbow trout ovarian follicles during in vivo oocyte developmental competence acquisition. Somatic cells were collected at 3 stages of oogenesis: NC1 stage follicles (LV, late vitellogenic, prophase I arrested oocytes, meiotically incompetent and developmentally incompetent, n=6), C1 stage follicles (PV, post-vitellogenic, prophase I arrested oocytes, meiotically competent and developmentally competent, n=16). Ovulatory follicles were also collected during oocyte maturation after in vivo induction (metaphase II arrested oocytes, developmentally fully competent, n=6).
2012-10-14 | E-GEOD-36602 | biostudies-arrayexpress
Project description:In this study we investigated the protein expression patterns during human oocyte in vitro and in vivo maturation (IVO) by single-cell quantitative proteomic analysis of 36 human oocytes. Among 2,094 proteins quantified in 34 oocytes (GV: 11 oocytes, IVM: 12 oocytes, IVO: 11 oocytes), 224 were differential between IVO and GV oocytes during in vivo maturation, and 61 between IVM and IVO oocytes.
2022-08-02 | PXD023366 | Pride
Project description:Somatic cells surrounding the oocyte were sampled at the following stages: developmentally incompetent or poorly competent prophase I oocytes (NC1 oocytes), developmentally competent prophase I oocytes (C1 oocytes), and developmentally competent metaphase II oocytes (C2 oocytes). NC1 samples were collected from late vitellogenic females (LV), C1 samples from post-vitellogenic females (PV), and C2 samples from females undergoing meiotic maturation (Germinal Vesicle Breakdown)
2012-10-14 | GSE36602 | GEO
Project description:Oocyte maturation is the foundation for developing healthy individuals of mammals. Upon germinal vesicle breakdown, oocyte meiosis resumes and the synthesis of new transcripts ceases. To quantitatively profile the transcriptomic dynamics after meiotic resumption throughout the oocyte maturation, we generated transcriptome sequencing data with individual mouse oocytes at three main developmental stages: germinal vesicle (GV), metaphase I (MI), and metaphase II (MII). When clustering the sequenced oocytes, results showed that isoform-level expression analysis outperformed gene-level analysis, indicating isoform expression provided extra information that was useful in distinguishing oocyte stages. Comparing transcriptomes of the oocytes at the GV stage and the MII stage, in addition to identification of differentially expressed genes (DEGs), we detected many differentially expressed transcripts (DETs), some of which came from genes that were not identified as DEGs. When breaking down the isoform-level changes into alternative RNA processing events, we found the main source of isoform composition changes was the alternative usage of polyadenylation sites. With detailed analysis focusing on the alternative usage of 3'-UTR isoforms, we identified, out of 3810 tested genes, 512 (13.7%) exhibiting significant switches of 3'-UTR isoforms during the process of moues oocyte maturation. Altogether, our data and analyses suggest the importance of examining isoform abundance changes during oocyte maturation, and further investigation of the pervasive 3'-UTR isoform switches in the transition may deepen our understanding on the molecular mechanisms underlying mammalian early development.
2021-10-05 | GSE178836 | GEO
Project description:Background: Aquaculture of the black tiger prawn Penaeus monodon remains severely constrained by an almost total dependence on wild-caught broodstock. Reliance on wild-caught broodstock stems, for the most part, from reduced reproductive potential of captive-reared females. Reproductive performance of captive-reared females is usually characterised by longer latency period, lower egg production, egg hatch rates and post-larval survivorship compared with their wild-caught counterparts. Improved understanding of the cellular and associated molecular events occurring during peneaid ovarian maturation could therefore be fundamental to improving reproductive success of captive-reared animals. Methodology/Principle Findings: In support of other studies, our histological analyses of developing oocytes revealed differences between wild-caught and captive-reared P. monodon, including reduced lipid accumulation in oocytes of captive-reared animals. We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals. Custom oligonucleotide microarrays were constructed and screened with transcripts derived from the ovary, cephalothorax and eyestalk from animals of all ovarian maturation stages. Ovarian maturation-related differential expression patterns were observed for 111 transcripts, with 53 transcripts displaying differential expression between wild-caught and captive-reared animals. Notably transcripts encoding vitellogenin - the major egg yolk protein precursor, and a lipid storage droplet protein (which we named pmLSD) which is involved in lipid accumulation, were found to be more highly expressed in wild-caught animals. pmLSD transcripts localise to pre-vitellogenic oocytes of wild-caught animals and the pmLSD protein is exclusively localised to the surface of lipid droplets of oocytes at vitellogenic and cortical rod stages. We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals. Target preparation and microarray hybridisation. Ovarian RNA samples from nine wild-caught animals representing six ovarian maturation stages (P, 2, 24, V, R, E) were used in microarray hybridisations. Similarly, RNA samples from three captive-reared animals representing four maturation stages (P, 24, V, E) were used in microarray hybridisations. For wild-caught animals, samples from each ovarian maturation stage were pooled into groups of four and five, enabling two hybridisations. For captive-reared animals, samples from each ovarian maturation stage from all three animals were pooled enabling one hybridisation for each stage. Importantly, as the four stages for captive-reared animals were (1) pre-ablation pre-vitellogenic, (2) post-ablation pre-vitellogenic, (3) post-ablation vitellogenic, (4) post-ablation vitellogenic with cortical rods, this arrangement allowed for 2 samples of captive-reared pre-vitellogenic and 2 samples of captive-reared vitellogenic, thereby enabling t-tests between samples, while also allowing analysis across the whole 4 stages via cluster analysis. All hybridisations were single channel hybridisations conducted using equal amounts of RNA pooled from each individual.
2011-09-01 | E-GEOD-31862 | biostudies-arrayexpress
Project description:Somatic cells surrounding the oocyte were sampled at the following stages: developmentally incompetent or poorly competent prophase I oocytes (NC1 oocytes), developmentally competent prophase I oocytes (C1 oocytes), and developmentally competent metaphase II oocytes (C2 oocytes). NC1 samples were collected from immature stage IV follicles, C1 samples from immature stage VI follicles, and C2 samples from in vitro matured stage VI follicles. Global transcriptional profiling was performed using somatic cells collected from xenopus ovarian follicles during in vivo oocyte developmental competence acquisition. Somatic cells were collected at 3 stages of oogenesis: early stage follicles (stage IV, vitellogenic, prophase I arrested oocytes, meiotically competent but developmentally incompetent, n=5), late stage follicles (stage VI, post-vitellogenic, prophase I arrested oocytes, meiotically competent and developmentally competent, n=5) and ovulatory follicles collected after in vitro maturation induction with hCG of post-vitellogenic follicles (metaphase II arrested oocytes, developmentally fully competent, n=5).
2012-10-14 | E-GEOD-36603 | biostudies-arrayexpress
Project description:Meiotic maturation is an intricate and precisely regulated process orchestrated 32 by various pathways and numerous proteins. However, little is known about the 33 proteome landscape during oocytes maturation. Here, we obtained the temporal 34 proteomic profiles of mouse oocytes during in vivo maturation. We successfully 35 quantified 4,694 proteins from 4,500 oocytes in three key stages (GV, GVBD, and 36 MII). In particular, we discovered the novel proteomic features during oocyte 37 maturation, such as the active Skp1–Cullin–Fbox pathway and an increase in 38 mRNA-decay-related proteins. Using functional approaches, we further identified the 39 key factors controlling the histone acetylation state in oocytes and the vital proteins 40 modulating meiotic cell cycle. Taken together, our data serve as a broad resource on 41 the dynamics occurring in oocyte proteome and provide important knowledge to 42 better understand the molecular mechanisms during germ cell development.
2022-05-26 | PXD034150 | iProX
Project description:12 single-base resolution methylomes of three life stages using WGBS
| PRJNA579962 | ENA