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Transcription profiles of oocytes during maturation and embryos during preimplantation development in vivo in the goat

ABSTRACT: Transcription profiles of oocytes during maturation and embryos during preimplantation development in vivo in the goat

PROVIDER: PRJNA532617 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8890470_1.fastq.gz	Fastqsanger.gz
	SRR8890470_2.fastq.gz	Fastqsanger.gz
	SRR8890480_1.fastq.gz	Fastqsanger.gz
	SRR8890480_2.fastq.gz	Fastqsanger.gz
	SRR8890471_1.fastq.gz	Fastqsanger.gz

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Transcription profiles of oocytes during maturation and embryos during preimplantation development in vivo in the goat

Project description:Preimplantation embryonic development is a dynamic, complex and precise regulated process to govern embryonic development and maintain embryo viability. The complete dynamics transcriptional activities during preimplantation development in the important domestic species goat is not available. Here, we performed RNA sequencing to establish a comprehensive transcriptional profiling of goat in vivo matured oocytes and preimplantation embryos. We found that the embryonic genome activation (EGA) in goat occurs at 16-cell stages, not previously defined at 8-cell stage, and showed much later EGA process compared to all other mammalian species. A total of 6,482 genes were identified to be significantly differentially expressed across all consecutive developmental stage comparisons and the important signaling pathways involved in each development transition were revealed. Additionally, we identified genes that appear to be transcribed only in a specific stage of development. Using weighted gene co-expression network analysis, we found 9 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified conserved key members (or hub genes) of the goat expressed gene networks. Their vast association with other embryonic genes suggests that they may have important regulatory roles in embryo development. Our cross-mammalian species transcriptomic comparisons demarcated both conserved and goat specific features of preimplantation development.

2020-03-01 | GSE129742 | GEO

Combined analysis of temporal metabolomics and transcriptomics reveals the metabolic patterns in goat oocytes during maturation

Project description:Well-balanced and orderly metabolism is a crucial prerequisite for promoting oogenesis. Involvement of single metabolites in oocyte development has been widely reported; however, the comprehensive metabolic framework controlling oocyte maturation is still lacking. In the present study, we employed an integrated temporal metabolomic and transcriptomic method to analyze metabolism in goat oocytes at key stages, revealing the global picture of the metabolic patterns during maturation. In particular, several significantly altered metabolic pathways during goat oocyte meiosis have been identified, including active serine metabolism, increased utilization of tryptophan, and marked accumulation of purine nucleotide. In summary, the current study not only provides multiple omics data resources for goat oocyte development, but also presents a novel perspective to understand the mechanisms regulating mammalian oogenesis.

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Chromatin remodeling in bovine oocytes and preimplantation embryos

Project description:Profiles of H3K4me3, H3K27ac, H3K27me3 and H3K9me3 in bovine GV oocytes and preimplantation embryos, and the characterization of chromatin accessibility in bovine blastocyst, inner cell mass and trophectoderm.

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Mass spectrometry of clinically-discarded preimplantation embryos

Project description:Clinically-discarded oocytes and preimplantation embryos at various stages were collected to perform proteome analysis.

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Chromatin remodeling in bovine oocytes and preimplantation embryos

Project description:Chromatin remodeling in bovine oocytes and preimplantation embryos

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Comprehensive analysis of H3K9me2 oocytes, together with DNA methylation and expression analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos

Project description:We report the first genome-wide landscape of H3K9me2 ChIP-seq profile in mouse oocytes. We also performed whole-genome bisulfite sequencing and RNA-seq analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos. Our findings illuminate the functional importance of G9a in preimplantation development and, in addition, pose a question on the proposed role for H3K9me2 in protection of the maternal genome from active CG demethylation.

2019-04-02 | GSE112320 | GEO

RNA m6A methylome in mouse oocytes and preimplantation embryos

Project description:N6-methyladenosine (m6A), the most prevalent internal modification in eukaryotic messenger RNA, plays diverse regulatory roles in many biological processes and is involved in a variety of physiological behaviors. Here we present the m6A methylome maps of mouse oocytes and preimplantation embryos by a low-input approach picoMeRIP-seq. We revealed that m6A was largely and dynamically deposited on maternal and zygotic RNAs during maternal-to-zygotic transition (MZT), especially on those encoding the factors essential for cell fate determination. m6A frequently marked the maternally-derived RNAs to be degraded and the genes that were activated during zygotic genome activation. Moreover, the RNAs derived from retrotransposons, such as MTA and MERVL, were heavily occupied by m6A. Collectively, our results provide a foundation for future studies exploring the regulatory roles of m6A in mammalian early embryo development.

2023-02-10 | GSE192440 | GEO

RNA m6A methylome in mouse oocytes and preimplantation embryos

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RNA m6A methylome in human oocytes and preimplantation embryos

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SMARTSeq_v4 paired end mRNA Seq of Kdm4a control mutant oocytes and preimplantation embryos

Project description:Purpose: The goal of this study was to generate paired-end mRNA Seq transcriptomes of control and Kdm4a mutant oocytes, 2-cell, 4-cell and 8-cell preimplantation embryos to study the dynamics of differentially expressed genes during early development Methods: MII oocytes were isolated from wildtype and Kdm4a knockout mice. 16 MII oocytes from each genotype were washed in M2 medim after zona pellucida removal, washed once in nuclease free water and directly lysed and cDNA prepared according to the manufacturers instructions. Meanwhile, control and knockout MII oocytes were also in vitro fertilised with Kdm4a knockout sperm to produce control (+/-) and maternal mutant (-/-) embryos, and cultured in KSOM EmbryoMax medium (Sigma). 16 embryos were staged each day and harvested according to control embryos. Healthiest mutants were chosen for comparison with minimal secondary effects arising from dead/dying embryos. Similar to oocytes, individual cDNA were prepared and amplified according to manufacturers instructions in nuclease free conditions. Conclusions: Our study represents a detailed analysis of differentially expressed genes in oocytes and embryos lacking maternal and endogenous Kdm4a, with sixteen biological replicates, generated by SMARTSeq v4 paired end RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles between the samples at each developmental stage. Our results show that there is a consistent downrgulation of zygotic genome activation (ZGA) genes in the mutant 2-cell embryos. Mutant 4 and 8-cell embryos have significant upregulation of minor ZGA genes giving us robust statistical significance. We conclude that Kdm4a is required for proper gene activation during maternal-to zygotic transition in conjuction with a permissive chromatin landscape.

2020-01-30 | GSE129731 | GEO

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