Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Analysis of The Mouse Oocyte、Cumulus cells and Blastocyst Transcriptomes From PM2.5 Exposure Group And Filtrated Air Group

ABSTRACT: Next Generation Sequencing Facilitates Analysis of The Mouse Oocyte、Cumulus cells and Blastocyst Transcriptomes From PM2.5 Exposure Group And Filtrated Air Group

PROVIDER: PRJNA625035 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11539660_1.fastq.gz	Fastqsanger.gz
	SRR11539660_2.fastq.gz	Fastqsanger.gz
	SRR11539661_1.fastq.gz	Fastqsanger.gz
	SRR11539661_2.fastq.gz	Fastqsanger.gz
	SRR11539662_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Next Generation Sequencing Facilitates Analysis of The Mouse Oocyte、Cumulus cells and Blastocyst Transcriptomes From PM2.5 Exposure Group And Filtrated Air Group

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare mouse NGS-derived oocyte、cumulus cell and blastocyst transcriptome profiling (RNA-seq) between PM2.5 exposure group and Filtrated air group Methods: mouse oocyte、cumulus cell and blastocyst mRNA profiles were generated by deep sequencing, in triplicate for each stage, using Illumina Hi-Seq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9). Genes with adjusted P < 0.05 and fold-change (FC) ≥ 2 were considered differentially expressed genes (DEGs). The oocyte transcriptome analysis showed that 467 DEGs (260 and 207 up- and down-regulated genes, respectively) were identified in the CAP group compared with the FA group. In the cumulus cell analysis, 592 DEGs (358 and 234 up- and down-regulated genes, respectively) were identified in the CAP group compared with the FA group. The blastocyst transcriptome analysis identified 448 DEGs (254 and 194 up- and down-regulated, respectively) in the CAP group compared with the FA group. Conclusions: Our study represents the first detailed analysis of mouse oocyte、cumulus cell and blastocyst transcriptomes, with biologic replicates, generated by RNA-seq technology between PM2.5 exposure group and Filtrated air group.

2020-04-14 | GSE148563 | GEO

Transcriptomic analysis of porcine blastocyst form cumulus oocyte complexes matured in coculture with porcine luteal cells

Project description:The transcriptome pattern in blastocyst that developed from cumulus oocyte complexes matured in coculture with porcine luteal cells was investigated.

2020-10-13 | GSE154587 | GEO

microRNA expression in bovine cumulus cells and its relation to oocyte developmental competence

Project description:microRNA sequencing to find differences in miRNA expression in bovine cumulus cells between cumulus pieces retrieved from COCs developing into a blastocyst after fertilization or remain uncleaved after fertilization

2017-03-13 | GSE94771 | GEO

Tight gene co-expression between oocyte and surrounding cumulus is critical for oocyte developmental competence

Project description:Cytoplasmic and nuclear maturation of oocytes as well as interaction with the surrounding cumulus cells are important features relevant to the acquisition of developmental competence. We used brilliant cresyl blue (BCB) to distinguish oocytes with low activity of the enzyme Glucose-6-Phosphate Dehydrogenase, and thus separated fully grown (BCB+) oocytes from those in the growing phase (BCB-). The BCB+ oocytes are twice as likely to produce a blastocyst in vitro compared to BCB- oocytes (P<0.01). We analyzed mitochondrial DNA (mtDNA) copy number in single oocytes and determined that BCB- oocytes have 1.3-fold more copies than BCB+ oocytes (P=0.004). We also interrogated the transcriptome of oocytes and surrounding cumulus cells of BCB+ versus BCB- oocytes. There was no differential transcript abundance of genes expressed in oocytes, but we identified 172 genes in cumulus cells with differential transcript abundance (FDR<0.05) based on the BCB staining of their oocyte. Differential gene co-expression analysis between BCB+ and BCB- oocytes and their surrounding cumulus cells revealed dynamic coordination of transcript abundance between both compartments of the cumulus-oocyte complex. We identified a subset of genes whose co-expression in fully grown oocytes (n=75) and their surrounding cumulus cells (n=108) compose a unique profile of the cumulus-oocyte complex. In conclusion, as oocytes transition from growing to fully grown, there is an increase in the likelihood of producing a blastocyst, a reduction of mtDNA copies and no systematic variation of transcript abundance. Cumulus cells present changes in transcript abundance, which reflects in a dynamic co-expression between oocyte and cumulus cells.

2022-03-28 | GSE199210 | GEO

RNA‐sequencing reveals genes linked with oocyte developmental potential in bovine cumulus cells

Project description:Cumulus cells provide an interesting biological material to perform analyses to understand the molecular clues determining oocyte competence. The objective of this study was to analyze the transcriptional differences between cumulus cells from oocytes exhibiting different developmental potentials following individual in vitro embryo production by RNA‐seq. Cumulus cells were allocated into three groups according to the developmental potential of the oocyte following fertilization: (1) oocytes developing to blastocysts (Bl+), (2) oocytes cleaving but arresting development before the blastocyst stage (Bl-), and (3) oocytes not cleaving (Cl-).

2024-03-12 | GSE261131 | GEO

Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart3]

Project description:Our aim was to identify at the level of cumulus cells any genes related to oocyte developmental competence 2-condition experiment: blastocyst (B) AND embryo of poor quality (E).

2012-12-10 | E-GEOD-37116 | biostudies-arrayexpress

Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart2]

Project description:Our aim was to identify at the level of cumulus cells any genes related to oocyte developmental competence 2-condition experiment: blastocyst (B) ans embryo of poor quality (E).

2012-12-10 | E-GEOD-37117 | biostudies-arrayexpress

Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart1]

Project description:Our aim was to identify at the level of cumulus cells any genes related to oocyte developmental competence three-condition experiment: blastocyst (B), embryo of poor quality (E) AND immature oocytes (VG).

2012-12-10 | E-GEOD-37110 | biostudies-arrayexpress

The bovine cumulus proteome of cumulus oocyte complexes that successfully matured or failed to mature after maturation in-vitro and in-vivo

Project description:The oocyte forms a complex with their somatic cumulus cells within the follicle throughout the preovulatory maturation steps. Cumulus cells support their oocyte not only through mechanical protection but also with a close bidirectional exchange of metabolites. Analysis of the oocytes cumulus gives the opportunity to explore non-invasively oocytal well-being and quality. In vitro maturation (IVM) is the first rate-limiting step in in vitro embryo production. Analysis of protein expression in cumulus cells around this critical step helps to explore the impact of maturation conditions and to examine an influence on maturational competence of the oocyte. The goal of this study was the comparison of the cumulus proteome of oocytes with and without maturational competence matured under in vivo and in vitro conditions. Therefore twenty cumulus samples corresponding to single oocytes were analysed. Half of the samples were matured in vivo and the other half in vitro. For each maturation group, cumulus from oocytes matured successfully (SM; n=5) and failed to mature (FM; n=5) were analysed.

2020-06-30 | PXD016679 | Pride

Resolvin E1 in follicular fluid acts as a potential biomarker and improves oocyte developmental competence by optimizing cumulus cells

Project description:<p>The metabolic profile of follicular fluid (FF) has been investigated to look for biomarkers for oocyte quality. Resolvin E1 (RvE1), a potent pro-resolving mediator, was reported to have protective action in cell function. The study aimed to examine the predictive value of RvE1 for oocyte quality and to explore the cellular mechanism of RvE1 in improving oocyte competence. Metabolic profiles of 80 FF samples showed a higher level of RvE1 in group A (blastocysts scored ≥ B3BC and B3CB according to Gardner's blastocyst scoring system, N=36) than that of group B (blastocysts scored < B3BC and B3CB, N=44, P=.0018). The receiver operating characteristic (ROC) curve analysis showed that RvE1 level in FF below 8.96 pg/ml (AUC:0.75; 95%CI: 0.64 – 0.86; P=.00012) could predict poor oocyte quality with speciﬁcity of 97.22%, suggesting RvE1 as a potential biomarker to exclude inferior oocytes. Besides, the level of RvE1 was found to be significantly lower in FF than in serum (57.49 to 17.62 pg/ml; P=.0037) and was gradually accumulated in the culture medium of cumulus cells (CCs) during cell culture, which indicated that RvE1 came from both blood exudates and local secretion. The in vitro experiment revealed the cellular mechanism of RvE1 in improving oocyte quality by decreasing the cumulus cell apoptotic rate and increasing cell viability and proliferation. It is the first time that the role of RvE1 in reproduction is explored. In conclusion, RvE1 is valuable as a potential exclusive biomarker for oocyte selection and plays a role in improving oocyte quality.</p>

2020-03-26 | MTBLS1488 | MetaboLights

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