Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence [scRNA-seq]

ABSTRACT: Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence [scRNA-seq]

PROVIDER: PRJNA926507 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23191500.fastq.gz	Fastqsanger.gz
	SRR23191600.fastq.gz	Fastqsanger.gz
	SRR23191700.fastq.gz	Fastqsanger.gz
	SRR23191800.fastq.gz	Fastqsanger.gz
	SRR23191900.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1304

Similar Datasets

Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence

Project description:Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence

| PRJNA926501 | ENA

Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence [bulk RNA-seq]

Project description:Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence [bulk RNA-seq]

| PRJNA926506 | ENA

Contribution of molecular actors from somatic origin to oocyte developmental competence acquisition, lessons from evolution

Project description:This SuperSeries is composed of the following subset Series: GSE36602: Transcriptional profiling of somatic cells differentiation throughout oocyte competence acquisition in rainbow trout ovarian follicles. GSE36603: Transcriptional profiling of somatic cells differentiation throughout oocyte competence acquisition in the xenopus ovarian follicles. GSE36604: Transcriptional profiling of cumulus cells differentiation throughout oocyte competence acquisition in the murine ovarian follicles. GSE36605: Transcriptional profiling of cumulus cells differentiation throughout oocyte competence acquisition in the bovine ovarian follicles. Refer to individual Series

2012-10-14 | E-GEOD-36617 | biostudies-arrayexpress

CPEB3 Maintains Developmental Competence of the Oocyte

Project description:CPEB3 Maintains Developmental Competence of the Oocyte

| PRJNA999673 | ENA

MiRNA expression profile in relation to oocyte developmental competence

Project description:The objective of this study was to identify the expression profile of miRNAs in porcine oocytes derived from follicles of different sizes using RNA high throughput sequencing technology. Oocytes were aspirated from large (3-6 mm) or small (<2 mm) ovarian follicles and tested for developmental competence and chromatin configurations. Small RNA libraries were constructed from both groups and then sequenced on an Illumina NextSeq500. Oocytes from large follicles showed higher developmental competence and different chromatin configuration compared to small oocyte group. In total, 167 and 162 known miRNAs were detected in large and small oocyte groups, respectively with 153 miRNAs were commonly expressed in both groups. In addition, 155 predicted novel miRNAs were detected and quantified. MiR-205, miR-16, miR-148a-3p, miR-125b, and let-7 family were among the top 10 highly abundantly expressed miRNAs in both oocyte groups. Further analysis showed that 8 miRNAs were differentially expressed (DE) between both groups (>2 fold change) with 4 up- and 4 down-regulated miRNAs in large compared to small oocyte group. Target gene prediction followed by KEGG pathway analysis revealed 46 pathways that were enriched with miRNA-target genes. Oocyte meiosis pathway and signaling pathways including FoxO, PI3K-Akt, TGFβ, and cAMP were predictably targeted by DE miRNAs. These results give more insights into the potential role of miRNAs in controlling oocyte developmental competence.

2019-02-13 | GSE122032 | GEO

Single ooplasm biopsy RNA-Seq reveals important and distinct pathways linked to oocyte competence

Project description:Oocyte competence is a complex process that is directly associated with the ability of oocyte to develop a newborn. The generation of a viable gamete has a multifactorial origin directly related to follicle and oocyte growth. Several dynamic changes in the follicle have driven the oocyte to success or failure, such as storage of metabolites, epigenetic modifications, and maternal RNAs, among others. However, little is known about the precise factors of maternal RNAs associated with oocyte competence, once these RNAs are consumed during maternal embryonic transition. To investigate the oocyte transcriptome landscape, we used a biopsy method to remove ~1.5% of ooplasm followed by a Single-ooplasm-biopsy RNA-Seq approach after retrospectively tracking the oocyte fate. We identified factors driving competence and the feasibility of the technique in obtaining enough amount of sample and high-quality sequencing results, enabling the model establishment. Furthermore, we integrated data from granulosa and cumulus cell transcriptome. Besides that, the first polar body methylation showed high similarities with pathways enriched in the ooplasm-biopsy transcriptome. In granulosa and ooplasm-biopsy with high-competence, we found MAPK and Oxytocin signaling enriched, while the process of necroptosis and ferroptosis were associated with low-competence oocytes. Deep analysis in the ooplasm-biopsy transcriptome, shows MYC as the highest up-regulated gene, and GNAS as a central hub gene in the network analysis. In addition, TIMP1, APOA1, EZR1, and STAT1 were key genes in the low-competence group of oocytes. Importantly, we found that metabolic alteration in the low-low-competence group was constantly found in all transcriptomes data, suggesting a metabolic disturbance inherited since the follicle environment which is amplified in cumulus cells after oocyte maturation.

2025-09-30 | GSE242970 | GEO

Oocyte developmental competence is instructed by H3.3 chaperone Hira complex

Project description:Reproductive success begins with a healthy egg (a competent oocyte). An oocyte acquires its developmental competence during oogenesis in preparation for accomplishing the critical developmental transition from completion of meiosis to initiation of early embryogenesis. Here we comprehensively characterised the maternal role of major subunits of Hira (i.e. Hira, Cabin1 and Zscan4) during oocyte-to-embryo transition.

2022-02-01 | GSE146894 | GEO

Melatonin mediates stress defense and improves development competence of bovine oocytes

Project description:Oocyte quality, which is directly related to reprogramming competence, is a major important limiting factor in animal cloning efficiency. Compared with oocytes matured in vivo, in vitro matured (IVM) oocytes exhibit lower oocyte quality and reprogramming competence primarily because of their higher levels of reactive oxygen species (ROS). In this study, we investigate whether supplementing the oocyte maturation medium with melatonin, a free radical scavenger, could improve oocyte quality and reprogramming competence. We found that 10−9 M melatonin effectively alleviated oxidative stress, markedly decreased early apoptosis levels, recovered the integrity of mitochondria, ameliorated the spindle assembly and chromosome alignment in oocytes, and significantly promoted subsequent cloned embryo development in vitro. We also analyzed the effects of melatonin on epigenetic modifications in bovine oocytes. Melatonin increased the global H3K9 acetylation levels, reduced the H3K9 methylation levels, and minimally affected DNA methylation and hydroxymethylation. Genome-wide expression analysis of genes affected by melatonin during oocyte maturation was conducted by high-throughput scRNA sequencing. We found that several important genes altered by melatonin were involved in oocyte stress defense. These genes included GSTP1, mitochondrial DNA polymerase POLG, mitochondrial ATP synthase ATP5E, centriole-enriched gene CEP295, spindle assembly-related gene TCTP, cytoprotection, and anti-apoptosis-related gene HSP27. Our results indicated critical roles of melatonin during bovine oocyte maturation and development.

2018-11-21 | GSE122738 | GEO

Transcription profiling of rat granulosa cell gene expression associated with oocyte developmental competence

Project description:Gene expression profiles of granulosa cells from rat ovarian follicles by Affymetrix rat whole genome array showed that twelve genes were up-regulated, while one gene down-regulated more than 1.5 folds in the normal developmental competence group compared with those in the poor developmental competence group. Gene ontology classification showed that the up-regulated genes included lysyl oxidase and nerve growth factor receptor associated protein 1, which are important in the regulation of protein-lysine 6-oxidase activity, and in apoptosis induction, respectively. The down-regulated genes included glycoprotein-4-beta galactosyltransferase 2, which is involved in the regulation of extracellular matrix organization and biogenesis. Experiment Overall Design: Immature rats were injected with eCG and 24h thereafter with anti-eCG antibody to induce follicular atresia or with pre-immune serum to stimulate follicle development. A high percentage (30-50%, normal developmental competence, NDC) of oocytes from eCG/pre-immune serum group developed to term after embryo transfer compared to those from eCG/anti-eCG (0%, poor developmental competence, PDC). Gene expression profiles of granulosa cells from the above oocyte-collected follicles were assessed by Affymetrix rat whole genome array.

2008-06-15 | E-GEOD-7697 | biostudies-arrayexpress

Transcription profiling of chicken oocytes to determine impact of oocyte competence on subsequent fertility

Project description:The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development. A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance. We use 4 different hen lines:; - one line of laying hens with 3 different samples: the just ovulated oocyte, the oocyte collected 24 hours before ovulation (F1 stage), and granulosa cells collected at the F1 stage. We could compare different tissue and developmental stages. - one line of hen with rapid growth speed; - two lines of laying hens; For the 3 last lines we used animals with different fertility levels. We collected the oocyte of the largest follicle before ovulation (F1). The aim of the study is to identify genes involved in fertility or early embryo mortality. Experiment Overall Design: 6 arrays - Gallus gallus

2008-11-08 | E-GEOD-7805 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data