GEO DataSets

(Submitter supplied) Advancing maternal age causes a progressive reduction in fertility. The decline in developmental competence of the oocyte with age is likely to be a consequence of multiple contributory factors. Loss of epigenetic quality of the oocyte should be considered as one factor, as epigenetic errors could impair early developmental events or programme adverse outcomes in offspring that manifest only later in life. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

88 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL13112

168 Samples

Download data: COV

(Submitter supplied) Advancing maternal age causes a progressive reduction in fertility. The decline in developmental competence of the oocyte with age is likely to be a consequence of multiple contributory factors. Loss of epigenetic quality of the oocyte should be considered as one factor, as epigenetic errors could impair early developmental events or programme adverse outcomes in offspring that manifest only later in life. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

80 Samples

Download data: COV

(Submitter supplied) Oocyte growth is a key step in forming mature eggs that are ready to be fertilized. The states and modifications of chromatin represent critical sources of information for this process. However, the dynamics and interrelations of these chromatin characteristics remain elusive. In this study, we developed an improved scCOOL-seq technique (iscCOOL-seq), which is a multi- omics, single-cell and single-base resolution method with high mapping rates, and explored the chromatin accessibility landscape and its relationship to DNA methylation in growing mouse oocytes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL21103

778 Samples

Download data: BW, TXT

(Submitter supplied) We have performed deep RNA-Seq and de novo transcriptome assembly at different stages of mouse oogenesis. This revealed thousands of novel non-annotated genes as well as alternative promoters for ~10% of reference genes expressed in oocytes, a large fraction of which coincide with transposable elements of the MaLR and ERVK families. We defined the oocyte DNA methylation landscape as composed of large-scale hyper- and hypo-methylated domains. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) We generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. We find that the major transitions in the oocyte transcriptome occur well before the de novo methylation phase; nevertheless, transcription level does correlate with rate of methylation. Conversely, timing of methylation of CpG islands (CGIs) correlates inversely with enrichment of histone modifications inhibitory to DNA methylation and dependence on histone 3 lysine-4 demethylases, implicating chromatin remodelling as a major determinant of methylation timing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL15103

16 Samples

Download data: TXT

(Submitter supplied) While the oocytes’ transcriptome is predominantly determined by maturation stage, transcripts related to specific pathways such as chromosome segregation, mitochondria and RNA processing are affected by age after in vitro maturation of denuded oocytes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

75 Samples

Download data: TSV, XLSX

(Submitter supplied) Study Question: What effects do maternal age and oocyte maturation stage have on the human oocyte transcriptome that may be associated with oocyte developmental potential? Summary Answer: Although polyadenylated transcript abundance changes during human oocyte maturation irrespective of age, young (YNG) and advanced maternal age (AMA) metaphase II (MII) oocytes exhibit divergent transcriptomes. What is known already: Maternal age and maturation stage affect oocyte polyadenylated transcript abundance in human oocytes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

20 Samples

Download data: CSV

(Submitter supplied) We optimised an in vitro culture model for mouse oocytes starting from immature oocytes to get mature oocytes and investigated the effect of oxygen concentrations on the cultured oocytes (5 % vs 20% oxygen). The cultured oocytes were size-selected in both conditions. We generated expression and methylation profiling (RNA-Seq, RRBS, PBAT) by high throughput sequencing from these size selected oocytes and compared the results with in vivo size oocytes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL15103 GPL11002

24 Samples

Download data: COV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bos taurus

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL18384 GPL13226

12 Samples

Download data: TXT

(Submitter supplied) Metabolic stress associated with negative energy balance in high producing dairy cattle and obesity in women is a risk factor for decreased fertility. Non-esterified fatty acids (NEFA) are involved in this pathogenesis as they jeopardize oocyte and embryo development. Growing evidence indicates that maternal metabolic disorders can disturb epigenetic programming, and more specifically DNA methylation, in the offspring. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

4 Samples

Download data: TXT

(Submitter supplied) Metabolic stress associated with negative energy balance in high producing dairy cattle and obesity in women is a risk factor for decreased fertility. Non-esterified fatty acids (NEFA) are involved in this pathogenesis as they jeopardize oocyte and embryo development. Growing evidence indicates that maternal metabolic disorders can disturb epigenetic programming, and more specifically DNA methylation, in the offspring. more...

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

8 Samples

Download data: TXT

(Submitter supplied) Developing female human germ cells undergo genome-wide epigenetic reprogramming, but de novo DNA methylation dynamics and their interplay with chromatin states and transcriptional activation in developing oocytes is poorly understood. Here, we developed a single-cell multi-omics sequencing method, scChaRM-seq, that enables simultaneous profiling of the DNA methylome, transcriptome, and chromatin accessibility in single human oocytes and ovarian somatic cells. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL20795

941 Samples

Download data: BW, TXT, XLSX

(Submitter supplied) Background: With the rapid development of assisted reproductive technology (ART), although ovulation induction has made great progress, the accompanying health risks should not be ignored. Epigenetic modifications play an important role during the development of gametes and embryos. Recently, the epigenetic abnormalities caused by superovulation have attracted increasing attention. The follicle-stimulating hormone (FSH) and human menopausal gonadotropin (hMG) are common gonadotropins used for superovulation and appropriate concentration of them might be necessary. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

40 Samples

Download data: BW

(Submitter supplied) Although it is well established that the ovarian reserve diminishes with increasing age, and that a woman’s age is correlated to lower oocyte quality, the interplay of a diminished reserve and age on oocyte developmental competence is not clear. After maturation, oocytes are mostly transcriptionally quiescent, and developmental competence prior to embryonic genome activation (EGA) relies on maternal RNA and proteins. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

35 Samples

Download data: CEL

(Submitter supplied) Maternal-effect mutations in components of the subcortical maternal complex (SCMC) of the human oocyte can cause early embryonic failure, gestational abnormalities and recurrent pregnancy loss. Enigmatically, they are also associated with DNA methylation abnormalities at imprinted genes in conceptuses, in the devastating gestational abnormality biparental complete hydatidiform mole (BiCHM) or in multi-locus imprinting disease (MLID). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

6 Samples

Download data: IDAT, TXT

(Submitter supplied) Mutations in components of the subcortical maternal complex (SMC) of the human oocyte are enigmatically associated with DNA methylation abnormalities specifically at imprinted genes in conceptuses, but the developmental timing, genomic extent and mechanistic details of these defects are unknown. Here, we show, by single-cell bisulphite sequencing, that mutation in human KHDC3L that causes recurrent hydatidiform mole results in a genome-wide deficit of de novo methylation in oocytes.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: COV

(Submitter supplied) One possible mechanism leading to the apparent polymorphic placenta-specific DMRs would be the failure to maintain allelic methylation during gestation. For a temporal comparison, we performed methylation profiling on first trimester chorionic villus sampling (CVS) and compared it with corresponding samples at term. This revealed that DNA methylation level at placenta-specific DMRs is highly stable between the two points. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by array

Platforms:

GPL13534 GPL21145

12 Samples

Download data: CSV

(Submitter supplied) Background: Early embryonic development is governed by maternal transcripts stored within the oocyte during oogenesis. Transcriptional activity of the oocyte ultimately dictates its developmental potential and may be influenced by maternal age, resulting in reduced competence of oocytes derived from women of advanced age, compared with the young. In the current study, RNA-Seq was used to perform transcriptome profiling of human GV and MII oocytes derived from young and advanced maternal age women. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

21 Samples

Download data: XLSX

(Submitter supplied) Ovarian aging is characterized by the progressive depletion of primordial follicle reserve, leading to irregular patterns of ovulation and menopause. The basic mechanisms that underlie the ovarian aging and follicle decline is unknown. We sought to explore the role of cellular senescence and epigenomic mechanisms in ovarian aging. Here, we present the transcriptomic changes observed in the ovaries with age using the age groups 3mo, 6mo, 9mo and 12mo (n=5 per group except for 12mo which has an n=4). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16417

19 Samples

Download data: TXT