Transcriptome Analysis of TubA Effects on Oocytes Development in Mice
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE135003 | GEO | 2022/01/01
REPOSITORIES: GEO
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Project description:In our previous study, we observed that Tub-A treatment induced an increased level of the acetylation of alpha-tubulin, and a failure of spindle migration and actin cap formation. Most Tub-A treated oocytes were arrested in an MI-like or a GVBD-like stage and decreased mTOR (spindle formation factor) and mDia1 (inhibitor of actin assembly) in an HDAC6 expression-dependent manner. We wonder if TubA only affects HDAC6 expression. Therefore the purpose of this study is to clarify the cause of the phenomenon through RNA-seq analysis.
2018-11-30 | GSE115008 | GEO
Project description:STUDY QUESTION: Does maternal age affect the maturated oocyte quality and the fol-lowing development after fertilization in human? SUMMARY ANSWER: Maternal age affects the quality of maturated oocytes by altering the stored mRNA levels in human, such as TOP2B. WHAT IS KNOWN ALREADY: Intracellular mRNAs in maturated oocytes are tran-scripted from the maternal genome during oogenesis and important for the zygotic genome activation (ZGA) after fertilization. Microarray data showed that maternal age affected polyadenylated transcript abundance in human oocytes. These genes are involved in in signaling pathway related to cell cycle regulation, chromosome alignment. However, which genes are the key genes affected by maternal age and important for the development after fertilization had not been reported. Therefore, single-cell RNA sequencing (scRNA-Seq) technology is employed in this study to screen the key genes affected by maternal age in human maturated oocytes. STUDY DESIGN, SIZE, DURATION: We isolated mRNA from maturated (MII) oo-cytes donated by IVF or ICSI patients (three oocytes from young (≤ 30 years) and three oocytes from advanced maternal age (≥ 40 years) patients) undergoing controlled ovarian stimulation. Thus, a total of six maturated oocytes were individually processed for scRNA-seq analysis. The key genes screened from scRNA-seq analysis are confirmed using mouse model. PARTICIPANTS/MATERIALS, SETTING, METHODS: Patients undergoing infertility treatment at the Yuhuangding Hospital of Yantai underwent ovarian stimulation with FSH and received hCG for final follicular maturation prior to ul-trasound guided oocyte retrieval. We isolated RNA, generated single cell RNA-seq librar-ies (Smart-Seq2) and sequenced by Illumina Hiseq X-ten platform with 150 bp paired-end. Bioinformatics analysis of the sequencing data was done to find the biological processes and key genes that led to the decline in the quality of oocytes with advanced maternal age. To validate the findings, we used mouse model and validated candidate genes by RT-PCR and knockdown experiments. MAIN RESULTS AND THE ROLE OF CHANCE: We identified 1439 genes differentially expressed between older and younger women's maturated oocytes (|foldchange|>2, P < 0.05). These genes are significantly enriched with annotations related to transporter activity, cytoskeleton, oxidative stress, catalytic activity, immune function, cellular senescence and biosynthesis. The key candidate gene TOP2B was found by protein interaction network analysis, and knockdown verification on young mouse maturated oocytes showed that TOP2B was a key gene affecting the oocyte quality and disturbing early embryo development. LARGE SCALE DATA Raw data from this study can be accessed through GSE. LIMITATIONS, REASONS FOR CAUTION: The human maturated oocytes used in this study were from patients with different causes of infertility and may affect oocyte gene expression. In addition, the study was based on a lim-ited number of patients, and there are possible natural biological variance existed in human samples. WIDER IMPLICATIONS OF THE FINDINGS: For the first time, we used scRNA-seq to detect global gene transcriptome of maturated oocytes in young and older women. These results are useful to indicate the molecular mechanisms of female ovary aging and establishing a criterion to evaluate the quality of oocytes in women with advanced maternal age. STUDY FUNDING/COMPETING INTERESTS: This research was supported by the National Key Research and Development Program of China (2018YFC1004304, 2016YFA0100203), Medical and Health Science Technology Development Plan Project of Shandong Province (Grant#. 2017WS566). There are no competing interests.
2019-01-19 | GSE125300 | GEO
Project description:Transcriptome Analysis of TubA Effects on Oocytes Development in Mice
| PRJNA557119 | ENA
Project description:Affymetrix gene expression profiling in cumulus cells (CC) retrieved from patients undergoing GnRH agonists and GnRH antagonists IVF treatment. Oocytes from three different maturity stages were considered: metaphase I oocytes (MI), nonfertilized metaphase II (MII) oocytes (MII-NF) and MII oocytes developed to blactocyst stage embryo (MII-BL).
2013-09-13 | GSE34230 | GEO
Project description: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. Participants/Materials and Methods: Cumulus dissection from donated oocytes was performed. GV and MII oocytes underwent deep RNA sequencing using the SMART-Seq v4 Ultra Low Input RNA protocol (Takara-Clontech, USA) and Nextera XT DNA library preparation kit (Illumina, USA). Data processing, quality assessment and bioinformatics analysis were performed using source-software, including FastQC, HISAT2, StringTie, edgeR and DAVID. Results: Following deep single-cell RNA-Seq on GV and MII oocytes, hundreds of transcripts were significantly differentially expressed between young maternal age (YMA) and advanced maternal age (AMA) groups, with the most significant biological processes relating to mitochondrial reserves. The GV to MII transition shares common biological processes between young and AMA groups, however, some genes involved in mitochondria function were altered during ageing. A decrease in mitochondrial-related transcripts was also observed during the GV to MII transition. However, there was a much greater reduction of mitochondrial-related transcripts in MII oocytes of AMA. This observation was confirmed when YMA MII oocytes were compared with the AMA MII group with mitochondrial-related transcripts being significantly higher expressed in the YMA group, including biological processes, such as mitochondrial electron transport and ATP biosynthetic process. These results indicate a higher energy potential in YMA MII oocytes that is decreased with age. Other significantly higher biological processes in the YMA MII group include transcripts involved in the regulation of ubiquitin-dependent degradation. Lack of these transcripts could lead to a non-appropriate removal of oogenesis remnants following fertilisation in the AMA MII group. Discussion: Understanding reproductive ageing effects at the RNA level in human oocytes may reveal differences in the mechanisms regulating the GV to MII transition that impact on oocyte quality in YMA and AMA patients. Further investigations of the up-/down-regulated transcripts during ageing could guide and improved IVF outcomes for AMA patients.
2022-01-11 | GSE164371 | GEO
Project description:We profiled transcriptomes from mouse GV, MII oocytes and 1 cell embryos and Hamster oocytes.
2017-05-15 | GSE86470 | GEO
Project description:In this study, we used tandem mass tag (TMT)-based quantitative approach to acquire proteomic profiles of porcine GV and MII oocytes and MII oocytes vitrified at the GV stage.
2021-07-01 | PXD023107 | Pride
Project description:Affymetrix gene expression profiling in cumulus cells (CC) retrieved from patients undergoing GnRH agonists and GnRH antagonists IVF treatment. Oocytes from three different maturity stages were considered: metaphase I oocytes (MI), nonfertilized metaphase II (MII) oocytes (MII-NF) and MII oocytes developed to blactocyst stage embryo (MII-BL). From 4 GnRH agonist treated patients, CC MI, CC MII-NF and CC MII-BL samples were collected; from 5 GnRH agonist and 6 GnRH antagonist treated patients, CC MII-NF and CC MII-BL samples were collected; and from 2 GnRH agonist and 4 GnRH antagonist treated patients, CC MI and CC MII-BL were collected. Altogether, 10 CC MI, 15 CC MII-NF and 21 CC MII-BL were collected and considered for transcriptome analysis.
2013-09-13 | E-GEOD-34230 | biostudies-arrayexpress
Project description:We analyzed the functions of BTG family proteins in maternal mRNA degradation in mouse oocytes. By comparing the degradation of transcripts in WT oocytes and KO oocytes, we are able to know the defects in maternal mRNA clearance in BTG4-deleted oocytes, and identified the BTG4 target genes in oocyte cyplasmic maturation. 2 WT oocyte samples at GV stage, 2 WT oocyte samples at MII stage, 2 Btg4-/- oocyte samples at GV stage and 2 Btg4-/- oocyte samples at MII stage?2 WT embryo samples at zygote stage, 2 WT embryo samples at 2-cell stage, 2 Btg4-/- embryo samples at zygote stage and 2 Btg4-/- embryo samples at 2-cell stage , and a WT GV oocyte, a WT MII oocyte, a Erk-/- GV oocyte and a Erk-/- MII oocyte are performed RNA sequencing.
2016-03-16 | E-GEOD-71257 | biostudies-arrayexpress
Project description:To study the role of the protein YTHDF2 during female gametogenesis, its gene was conditionally deleted in oocytes. Total RNA samples from YTHDF2 deficient GV and MII oocytes (and control oocytes) were subjected to array profiling.
2018-02-12 | E-MTAB-5576 | biostudies-arrayexpress