Ontology highlight
ABSTRACT:
PROVIDER: PRJNA600817 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10875338_1.fastq.gz | Fastqsanger.gz | |||
| SRR10875338_2.fastq.gz | Fastqsanger.gz | |||
| SRR10875339_1.fastq.gz | Fastqsanger.gz | |||
| SRR10875339_2.fastq.gz | Fastqsanger.gz | |||
| SRR10875340_1.fastq.gz | Fastqsanger.gz |
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Project description:The wide application of pig disease model has caused a surge of interest in the study of derivation of pig induced pluripotent cells (iPSCs). Here we performed genome-wide analysis of gene expression profiling by RNA-seq and small RNA-seq and DNA methylation profile by MeDIP-seq in pig iPSCs through comparison with somatic cells. We identified mRNA and microRNA transcripts that were specifically expressed in pig iPSCs. We then pursued comprehensive bioinformatics analyses, including functional annotation of the generated data within the context of biological pathways, to uncover novel biological functions associated with maintenance of pluripotency in pig. This result supports that pig iPS have transcript profiles linked to ribosome, chromatin remodeling, and genes involved in cell cycle that may be critical to maintain their pluripotency, plasticity, and stem cell function. Our analysis demonstrates the key role of RNA splicing in regulating the pluripotency phenotype of pig cells. Specifically, the data indicate distinctive expression patterns for SALL4 spliced variants in different pig cell types and highlight the necessity of defining the type of SALL4 when addressing the expression of this gene in pig cells. MeDIP-seq data revealed that the distribution patterns of methylation signals in pig iPS and somatic cells along the genome. We identify 25 novel porcine miRNA, including pluripotency-related miR-302/367cluster up-regulated in pig iPSCs. At last, we profile the dynamic gene expression signature of pluripotent genes in the preimplantation development embryo of pig. The resulting comprehensive data allowed us to compare various different subsets of pig pluripotent cell. This information provided by our analysis will ultimately advance the efforts at generating stable naive pluripotency in pig cells.
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Project description:We specifically deleted Mettl14 in mouse uterus using the Pgr-Cre driver. To portray the molecular mechanism for Mettl14 function in mouse uterus, uterine tissues were collected from Mettl14f/f and Mettl14d/d mice on gestational day 4 and subjected to single-cell RNA-seq analysis.
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Project description:Single cell RNA-seq study of wild type and Hox mutant developing uterus
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Project description:The pig skin architecture and physiology are similar to these of humans. Thus, the pig model is valuable for studying skin biology and testing therapeutics for skin diseases. The single-cell RNA sequencing technology allows quantitatively analyzing cell types, cell states, signaling, and receptor-ligand interactome at single-cell resolution and at high throughput. scRNA-Seq has been used to study mouse and human skins. To maximize the use of pig skin as a model system to study skin biology, we described a robust method for isolating and cryo-preserving pig single cells for scRNA-Seq. We showed that pig skin could be efficiently dissociated into single cells with high cell viability using the Miltenyi Human Whole Skin Dissociation kit and the Miltenyi gentleMACS Dissociator. In addition, we showed that the subsequent single cells could be cryopreserved using DMSO without causing additional cell death, cell aggregation, or changes in gene expression profiles. Using the developed protocol, we were able to identify all the major skin cell types. The protocol and results from this study will be very valuable for the skin research scientific community.
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Project description:Self-renewing Endometrial Epithelial Organoids of the Human Uterus [single-cell RNA-seq data]
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Project description:Single-cell RNA-seq analysis of Mettl14d/d mouse uterus compared to Mettl14f/f mouse uterus on gestational day 4
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Project description:<p>The ovaries and uterus are crucial reproductive organs in mammals, and their coordinated development ensures the normal development of sexual maturity and reproductive capacity. This study aimed to comprehensively capture the different physiological stages of the goat's sexual maturation by selecting four specific time points. We collected samples of ovarian and uterine tissues from five female Jining Gray goats at each time point: after birth (D1), 2-month-old (M2), 4-month-old (M4) and 6-month-old (M6). By combining transcriptomic sequencing of 40 samples (including rRNA-depleted RNA-seq libraries with 3607.8 million reads and miRNA-seq libraries with 444.0 million reads) and metabolomics analysis, we investigated the transcriptomic mechanisms involved in reproductive regulation in the ovary and uterus during sexual maturation, as well as the changes in metabolites and their functional potential. Additionally, we analyzed blood hormone indices and uterine tissue sections to examine temporal changes. These datasets will provide a valuable reference for the reproductive regulation of the ovary and uterus, as well as the regulation of metabolites during sexual maturation in goats.</p><p><br></p><p><strong>Uterine data</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS9795' rel='noopener noreferrer' target='_blank'><strong>MTBLS9795</strong></a>.</p><p><strong>Ovarian data</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS9794' rel='noopener noreferrer' target='_blank'><strong>MTBLS9794</strong></a>.</p>
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Project description:<p>The ovaries and uterus are crucial reproductive organs in mammals, and their coordinated development ensures the normal development of sexual maturity and reproductive capacity. This study aimed to comprehensively capture the different physiological stages of the goat's sexual maturation by selecting four specific time points. We collected samples of ovarian and uterine tissues from five female Jining Gray goats at each time point: after birth (D1), 2-month-old (M2), 4-month-old (M4) and 6-month-old (M6). By combining transcriptomic sequencing of 40 samples (including rRNA-depleted RNA-seq libraries with 3607.8 million reads and miRNA-seq libraries with 444.0 million reads) and metabolomics analysis, we investigated the transcriptomic mechanisms involved in reproductive regulation in the ovary and uterus during sexual maturation, as well as the changes in metabolites and their functional potential. Additionally, we analyzed blood hormone indices and uterine tissue sections to examine temporal changes. These datasets will provide a valuable reference for the reproductive regulation of the ovary and uterus, as well as the regulation of metabolites during sexual maturation in goats.</p><p><br></p><p><strong>Ovarian data</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS9794' rel='noopener noreferrer' target='_blank'><strong>MTBLS9794</strong></a>.</p><p><strong>Uterine data</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS9795' rel='noopener noreferrer' target='_blank'><strong>MTBLS9795</strong></a>.</p>
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