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| Status |
Public on Jul 27, 2023 |
| Title |
Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The molecular mechanisms controlling the transition from meiotic arrest (germinal vesicle stage) to meiotic resumption (germinal vesicle breakdown stage) in mammalian oocytes have not been fully elucidated. Single-cell omics technology provides a new opportunity to decipher the early molecular events of oocyte maturation in mammals. Here we focused on analyzing oocytes that are collected from antral follicles of porcine puberty ovary. We used single-cell M&T-seq technology to analyze the nuclear DNA methylome and cytoplasmic transcriptome in parallel for 62 oocytes. We developed a package of pipelines for single-cell methylomics analysis, namely methyConcerto, to specifically and comprehensively characterize the methylation state and allele-specific methylation events for a single cell. We also performed 10X Genomics single-cell transcriptomic analyses to explore the bi-directional cell-cell communications within antral follicles. We characterized the gene expression and DNA methylation programs of individual oocytes in porcine antral follicle, thereby enabled defining two distinct types of oocytes, one of which is significantly more poised for maturation. Significantly differentially expressed or allele-specifically methylated genes were enriched in “RNA metabolism”, “oocyte meiosis” important signaling pathways, e.g., HIF-1/Ras/mTOR/Phospholipase D/ErbB signaling pathways etc. These results are in concert with the cellular communication results. We further confirmed Insulin Receptor Substrate-1 (IRS-1) in insulin signaling pathway is a key regulator of germinal vesicle stage oocyte maturation by in vitro maturation experiments. Our study provides new insights into the regulatory mechanisms between meiotic arrest and meiotic resumption in mammalian oocytes. We also provide a new analytical package for future single-cell methylomics study.
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| Overall design |
Here, we analyzed oocytes that are collected from five antral follicular stages of pubertal ovaries. We used single-cell M&T-seq technology that analyze the nuclear DNA methylome and cytoplasmic transcriptome in parallel for 62 oocytes. We also performed scRNA-seq of somatic cells within antral follicles, to explore the bi-directional interactions and reveal the role of granulosa cells in oocyte maturation. At last, in vitro maturation experiments were performed to verify the key regulators in oocyte maturation.
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| Contributor(s) |
Yuan X, Chen N, Feng Y, Tian Y, Wang J, Jiang Y, He D, Li J, Gao F |
| Citation(s) |
37480402 |
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| Submission date |
Jun 05, 2023 |
| Last update date |
Jul 27, 2023 |
| Contact name |
Epigenomics Gao |
| E-mail(s) |
gao_epigenomics@126.com
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| Organization name |
Chinese Academy of Agricultural Sciences
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| Department |
Agricultural Genomics Institute at Shenzhen
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| Street address |
Dapeng district
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| City |
Shenzhen |
| ZIP/Postal code |
518108 |
| Country |
China |
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| Platforms (1) |
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| Samples (55)
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| GSM7446098 |
oocyte from antral follicle stage 1, gilt 201, rep1 |
| GSM7446099 |
oocyte from antral follicle stage 1, gilt 201, rep2 |
| GSM7446100 |
oocyte from antral follicle stage 1, gilt 201, rep3 |
| GSM7446101 |
oocyte from antral follicle stage 1, gilt 205, rep1 |
| GSM7446102 |
oocyte from antral follicle stage 1, gilt 801, rep1 |
| GSM7446103 |
oocyte from antral follicle stage 1, gilt 801, rep2 |
| GSM7446104 |
oocyte from antral follicle stage 1, gilt 801, rep3 |
| GSM7446105 |
oocyte from antral follicle stage 1, gilt 803, rep1 |
| GSM7446106 |
oocyte from antral follicle stage 1, gilt 803, rep2 |
| GSM7446107 |
oocyte from antral follicle stage 1, gilt 803, rep3 |
| GSM7446108 |
oocyte from antral follicle stage 1, gilt 803, rep4 |
| GSM7446109 |
oocyte from antral follicle stage 2, gilt 201, rep1 |
| GSM7446110 |
oocyte from antral follicle stage 2, gilt 201, rep2 |
| GSM7446111 |
oocyte from antral follicle stage 2, gilt 201, rep3 |
| GSM7446112 |
oocyte from antral follicle stage 2, gilt 205, rep1 |
| GSM7446113 |
oocyte from antral follicle stage 2, gilt 801, rep1 |
| GSM7446114 |
oocyte from antral follicle stage 2, gilt 801, rep2 |
| GSM7446115 |
oocyte from antral follicle stage 2, gilt 801, rep3 |
| GSM7446116 |
oocyte from antral follicle stage 2, gilt 801, rep4 |
| GSM7446117 |
oocyte from antral follicle stage 2, gilt 803, rep1 |
| GSM7446118 |
oocyte from antral follicle stage 2, gilt 803, rep2 |
| GSM7446119 |
oocyte from antral follicle stage 2, gilt 803, rep3 |
| GSM7446120 |
oocyte from antral follicle stage 2, gilt 803, rep4 |
| GSM7446121 |
oocyte from antral follicle stage 3, gilt 201, rep1 |
| GSM7446122 |
oocyte from antral follicle stage 3, gilt 201, rep2 |
| GSM7446123 |
oocyte from antral follicle stage 3, gilt 201, rep3 |
| GSM7446124 |
oocyte from antral follicle stage 3, gilt 201, rep4 |
| GSM7446125 |
oocyte from antral follicle stage 3, gilt 205, rep1 |
| GSM7446126 |
oocyte from antral follicle stage 3, gilt 205, rep2 |
| GSM7446127 |
oocyte from antral follicle stage 3, gilt 801, rep1 |
| GSM7446128 |
oocyte from antral follicle stage 3, gilt 803, rep1 |
| GSM7446129 |
oocyte from antral follicle stage 3, gilt 803, rep2 |
| GSM7446130 |
oocyte from antral follicle stage 3, gilt 803, rep3 |
| GSM7446131 |
oocyte from antral follicle stage 3, gilt 803, rep4 |
| GSM7446132 |
oocyte from antral follicle stage 4, gilt 201, rep1 |
| GSM7446133 |
oocyte from antral follicle stage 4, gilt 205, rep1 |
| GSM7446134 |
oocyte from antral follicle stage 4, gilt 205, rep2 |
| GSM7446135 |
oocyte from antral follicle stage 4, gilt 801, rep1 |
| GSM7446136 |
oocyte from antral follicle stage 4, gilt 801, rep2 |
| GSM7446137 |
oocyte from antral follicle stage 4, gilt 801, rep3 |
| GSM7446138 |
oocyte from antral follicle stage 4, gilt 801, rep4 |
| GSM7446139 |
oocyte from antral follicle stage 4, gilt 803, rep1 |
| GSM7446140 |
oocyte from antral follicle stage 4, gilt 803, rep2 |
| GSM7446141 |
oocyte from antral follicle stage 4, gilt 803, rep3 |
| GSM7446142 |
oocyte from antral follicle stage 4, gilt 803, rep4 |
| GSM7446143 |
oocyte from antral follicle stage 5, gilt 201, rep1 |
| GSM7446144 |
oocyte from antral follicle stage 5, gilt 201, rep2 |
| GSM7446145 |
oocyte from antral follicle stage 5, gilt 201, rep3 |
| GSM7446146 |
oocyte from antral follicle stage 5, gilt 205, rep1 |
| GSM7446147 |
oocyte from antral follicle stage 5, gilt 205, rep2 |
| GSM7446148 |
oocyte from antral follicle stage 5, gilt 205, rep3 |
| GSM7446149 |
oocyte from antral follicle stage 5, gilt 803, rep1 |
| GSM7446150 |
oocyte from antral follicle stage 5, gilt 803, rep2 |
| GSM7446151 |
oocyte from antral follicle stage 5, gilt 803, rep3 |
| GSM7446152 |
oocyte from antral follicle stage 5, gilt 803, rep4 |
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| This SubSeries is part of SuperSeries: |
| GSE235731 |
Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs |
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| Relations |
| BioProject |
PRJNA980139 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE234116_TPM.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
| GSE234116_raw_counts.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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