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Transcriptome analysis of gene expression in young and aged oocyte samples (RNA-Seq)

ABSTRACT: Transcriptome analysis of gene expression in young and aged oocyte samples (RNA-Seq)

PROVIDER: PRJNA688471 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13324463_1.fastq.gz	Fastqsanger.gz
	SRR13324463_2.fastq.gz	Fastqsanger.gz
	SRR13324464_1.fastq.gz	Fastqsanger.gz
	SRR13324464_2.fastq.gz	Fastqsanger.gz
	SRR13324465_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of gene expression in young and aged oocyte samples (RNA-Seq)

Project description:The purpose of this study are to compare transcriptome profiling (RNA-seq) data in young and aged oocytes,and to evaluate the transcriptome alterataions after rapamycin treatment in aged oocytes. The sequencing libraries from young, aged and rapa-treated oocytes were generated according to protocols of Smart-seq2.Then cDNA libraries were checked on a Bioanalyzer instrument (Agilent) and the passed samples were finally sequenced by Illumina novaseq for 150-bp paired-end reads. RNA-seq data were aligned to the mouse genome mm10 using STAR 2-pass mode with the annotations of Ensembl version 90 and parameter ‘--outFilterMismatchNmax 6’. SAMtools was used to extract uniquely mapped reads with mapping quality more than or equal to 20. The number of reads mapped to each gene was counted using the HTSeq python package with the ‘union’ overlap resolution mode and –stranded = no. The expressions of genes were quantified as RPKM by edgeR . Genes with RPKM more than 1 in at least three control samples were considered as expressed. Only expressed genes were kept for the subsequent analysis. Differentially expressed genes were identified by DESeq2 using two criteria: fold change of expression should be higher than 2 and the adjusted p-value should be lower than 0.05. Enriched GO terms were obtained with P-value less than 0.05 from DAVID.The analysis of data revealed a total of 454 genes were significant differentially expressed during oocyte aging,of which, 242 genes were upregulated and 212 downregulated in aged oocytes.GO enrichment analysis showed that some of gene expressions were related to oxidation-reduction process, cell cycle, translation and mitochondrial functions. However, gene expression analysis revealed only 4 differently expressed genes between oocyte from rapa-treated and reproductively aged mice.

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Rejuvenation of aged oocyte through exposure to young follicular microenvironment

Project description:Reproductive aging is a major cause of fertility decline, attributed to decreased oocyte quantity and competence. Follicular somatic cells play crucial roles in the growth and development of the oocyte by providing nutrients and regulatory factors. Here we investigated how oocyte quality is affected by its somatic cell environment by creating chimeric follicles, whereby an oocyte from one follicle was transplanted into and cultured within another follicle whose native oocyte was removed. Somatic cells within the chimeric follicle re-establish connections with the oocyte and support oocyte growth and maturation in a three-dimensional (3D) culture system. We show that young oocytes transplanted into aged follicles exhibited reduced meiotic maturation and developmental potential, whereas the young follicular environment significantly improved the rates of maturation, blastocyst formation and live birth of aged oocytes. Aged oocytes cultured within young follicles exhibited enhanced interaction with somatic cells, more youth-like transcriptome, remodelled metabolome, improved mitochondrial function, and enhanced fidelity of meiotic chromosome segregation. These findings provide the basis for a future follicular somatic cell-based therapy to treat age-associated female infertility.

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Project description:We report the gene expression changes in mobilized peripheral blood in aged, young, and aged/young samples cocultured in transwell. Restored samples refer to aged MPB co-cultured with young MPB in the transwell culture

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Aged, Young and Restored Samples from Mobilized Peripheral Blood [miRNA]

Project description:We report the miRNA expression in each CD34+ cells and their exosomes in mobilized peripheral blood in aged, young, and aged/young samples cocultured in transwell. Restored samples refer to aged MPB co-cultured with young MPB in the transwell culture.

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Rejuvenation of aged oocyte through exposure to young follicular microenvironment

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Aged, Young and Restored Samples from Mobilized Peripheral Blood

Project description:Aged, Young and Restored Samples from Mobilized Peripheral Blood

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Aged, Young and Restored Samples from Mobilized Peripheral Blood [mRNA]

Project description:Aged, Young and Restored Samples from Mobilized Peripheral Blood [mRNA]

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Aged, Young and Restored Samples from Mobilized Peripheral Blood [miRNA]

Project description:Aged, Young and Restored Samples from Mobilized Peripheral Blood [miRNA]

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Young and aged mouse bladders

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Hippocampal gene expression in aged and young HSD1 knockout mice

Project description:Mice deficient in the glucocorticoid-regenerating enzyme 11Î²-HSD1 resist age-related spatial memory impairment. To investigate the mechanisms/pathways involved, we used microarrays to identify differentially expressed hippocampal genes that associate with cognitive ageing and 11Î²-HSD1. Aged wild-type mice were separated into memory-impaired and unimpaired relative to young controls according to their performance in the Y-maze. All individual aged 11Î²-HSD1-deficient mice showed intact spatial memory. The majority of differentially expressed hippocampal genes were increased with ageing (e.g. immune/inflammatory response genes) with no genotype differences. However, the neuronal-specific transcription factor, Npas4 and immediate early gene, Arc were reduced (relative to young) in the hippocampus of memory-impaired but not unimpaired aged wild-type or aged 11Î²-HSD1-deficient mice. Quantitative RT-PCR and in situ hybridization confirmed reduced Npas4 and Arc mRNA expression in memory-impaired aged wild-type mice. These findings suggest that 11Î²-HSD1 may contribute to the decline in Npas4 and Arc mRNA levels associated with memory impairment during ageing, and that decreased activity of synaptic plasticity pathways involving Npas4 and Arc may, in part, underlie the memory deficits seen in cognitively-impaired aged wild-type mice. 20 samples, 5 groups of 4 biological replicates each. Young, Wild Type animals are overall controls

2015-11-23 | E-GEOD-68515 | biostudies-arrayexpress

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