Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA434577: Single-cell transcriptomics of human oocytes: environment-driven metabolic competition and compensatory mechanisms during oocyte maturation

来源: NCBI / GSE110798
提交时间: Feb 19 2018
释放时间: Apr 10 2018
最后更新时间: Mar 27 2019

概要: Aim: The mechanisms coordinating maturation with an environment-driven metabolic shift, a critical step in determining the developmental potential of human in vitro matured (IVM) oocytes, remains to be elucidated. Here, we explored the key genes regulating human oocyte maturation using single-cell RNA sequencing and illuminated the compensatory mechanism from a metabolic perspective by analyzing gene expression. Results: Three key genes that encode CoA-related enzymes were screened from the RNA sequencing data. Two of them, ACAT1 and HADHA, were closely related to the regulation of substrate production in the Krebs cycle. Dysfunction of the Krebs cycle was induced by decreases in the activity of specific enzymes. Further, the activator of these enzymes, the calcium concentration, was also decreased because of the failure of influx of exogenous calcium. Although release of endogenous calcium from the endoplasmic reticulum and mitochondria met the requirement for maturation, excessive release resulted in aneuploidy and developmental incompetence. High nicotinamide nucleotide transhydrogenase expression induced NADPH dehydrogenation to compensate for the NADH shortage resulting from the dysfunction of the Krebs cycle. Importantly, high NADP+ levels activated DPYD to enhance the repair of DNA double-strand breaks to maintain euploidy. Innovation: The present study shows for the first time that exposure to the in vitro environment can lead to the decline of energy metabolism in human oocytes during maturation but that a compensatory action maintains their developmental competence. Conclusions: In vitro maturation of human oocytes is mediated through a cascade of competing and compensatory actions driven by genes encoding enzymes.

项目整体设计: Investigated the transcriptome characteristics of human oocytes matured in vitro and in vivo to gain a transcriptome-level understanding of how oocytes mature and to illuminate the differences between human IVM and in vivo (IVO) matured oocytes at the transcript level.

GEN 数据集:
GEND000038
测序方法:
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细胞类型:
方案
生长方案: -
处理方案: growing environment: In vitro; growing environment: In vivo
提取方案: Oocytes were rinsed in Ca2+/Mg2+-free PBS solution and individually placed in 0.2-ml PCR tubes containing a 5-μl mixture of lysis buffer and RNase inhibitor. RNA from a single oocyte was amplified using the SMARTer Ultra Low RNA kit for Illumina sequencing.
建库方案: The cDNA library was generated as follows. The quantified cDNA (20 ng) was fragmented into 200-bp lengths by ultrasonic waves using a Bioruptor® Sonication System. The cDNA fragments then underwent end repair, adaptor addition and purification using AMPure XP Beads. The products with adaptors were amplified by PCR. The different samples were marked with different index tags. PCR amplification products were electrophoresed on 2% agarose gels, and 200–300-bp DNA fragments were recovered using the CWBIO Gel Extraction Kit (CW2302A, Cwbiotech, Inc., China) and dissolved in EB buffer. cDNA library quality was tested using an Agilent 2100 Bioanalyzer, and the effective concentration was quantified by quantitative real-time PCR.
测序信息
分子类型: poly(A)+ RNA
库的片段类型: PAIRED
库的链类型: -
测序平台: ILLUMINA
测序仪型号: Illumina HiSeq 2500
链特异性: Unspecific
样本
基本信息:
样本描述:
生物条件:
实验变量:
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质量评估:
数据来源 GEN样本编号 GEN数据集编号 系列编号 项目编号 样本编号 样本名称 生物样本编号 样本访问号 实验访问号 释放时间 提交时间 最后更新时间 物种 种族 族裔 年龄 年龄单位 性别 来源名称 组织 细胞类型 细胞亚型 细胞系 疾病 疾病状态 发育阶段 突变/变异 表型 Condition Detail 生长方案 处理方案 提取方案 建库方案 分子类型 库的片段类型 链特异性 库的链类型 加标(Spike-In) 测序方法 测序平台 测序仪型号 细胞数 测序片段数 碱基数 平均测序片段长度_1 平均测序片段长度_2 唯一比对率 多重比对率 覆盖度
文章
Single-Cell Transcriptomics of Human Oocytes: Environment-Driven Metabolic Competition and Compensatory Mechanisms During Oocyte Maturation.
Antioxidants & redox signaling . 2018-04-13 [PMID: 29486586]