Ontology highlight
ABSTRACT:
PROVIDER: PRJNA758601 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15663244_1.fastq.gz | Fastqsanger.gz | |||
| SRR15663244_2.fastq.gz | Fastqsanger.gz | |||
| SRR15663245_1.fastq.gz | Fastqsanger.gz | |||
| SRR15663245_2.fastq.gz | Fastqsanger.gz | |||
| SRR15663246_1.fastq.gz | Fastqsanger.gz |
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Project description:Conservation and species specificity are both unveiled in the reprogramming process of epigenetic modifications in early embryos. Pig is important agricultural livestock that closely related to human life and understanding the mechanisms of epigenetic reprogramming in porcine embryos could be assistive to the pig breeding industry and also informative to human embryo research. Nevertheless, current knowledge of epigenetic reprogramming in porcine embryos is elusive. We profile H3K4me3, H3K27me3, and H3K27ac modifications in porcine oocytes and preimplant embryos. Our data reveal the existence of unusual broad H3K4me3 domains not only in oocytes but also expanded in pre-ZGA embryos and demonstrates the extensive transitions of unusual broad H3K4me3 domains and their roles during embryogenesis. Notably, broad H3K27me3 and H3K27ac enriched domains are found to be preferably colocalized in these broad H3K4me3 domains when comparing to it in mice and human. By knocking down KDM5B in pig embryos, cleavage and developments were disrupted as demonstrated in mouse.
2022-07-08 | GSE163709 | GEO
Project description:Sperm-derived tsRNAs could act as acquired epigenetic factors and contribute to offspring phenotypes. However, the roles of specific tsRNAs in early embryo development remain to be elucidated. Here, by using pigs as a research model, we probed the tsRNA dynamics during spermatogenesis and sperm maturation, and demonstrated the delivery of tsRNAs from semen-derived exosomes to spermatozoa. By microinjection of the antisense sequence into in vitro fertilized oocytes and subsequent single-cell RNA-sequencing of embryos, we identified a specific functional tsRNA group (Gln-TTGs) that participate in the early cleavage of porcine preimplantation embryos, probably by regulating cell cycle-associated genes. Thus, specific tsRNAs present in mature spermatozoa play significant roles during preimplantation embryo development.
2020-07-13 | PXD019054 | Pride
Project description:This study identified circRNA-1572, which is delivered by sperm into the oocyte during fertilization, whose downregulation resulted in developmental arrest and inhibition of ZGA during porcine embryogenesis. Moreover, we elucidated that sperm-derived circRNA-1572 competitively binds to bta-miR-2478-L-2 through a “sponge” mechanism to target and regulate cyclin B2 expression, thereby modulating the distribution of F-actin in early pig embryos, ensuring proper chromosome segregation during mitosis, and facilitating normal embryo cleavage, maternal RNA degradation (MRD), and ZGA.
2025-05-29 | GSE288539 | GEO
Project description:This study identified circRNA-1572, which is delivered by sperm into the oocyte during fertilization, whose downregulation resulted in developmental arrest and inhibition of ZGA during porcine embryogenesis. Moreover, we elucidated that sperm-derived circRNA-1572 competitively binds to bta-miR-2478-L-2 through a “sponge” mechanism to target and regulate cyclin B2 expression, thereby modulating the distribution of F-actin in early pig embryos, ensuring proper chromosome segregation during mitosis, and facilitating normal embryo cleavage, maternal RNA degradation (MRD), and ZGA.
2025-05-29 | GSE288538 | GEO
Project description:During embryonic development in mice, global deficiency of Trim71 (Trim71-KO) leads to defects in vascular development of the yolk sac and impaired primitive erythropoiesis. These phenotypes start to become apparent at E9.5. We analyzed changes in gene expression by single-cell RNA-sequencing (scRNA-seq) in whole Trim71-KO embryos compared to wildtype embryos at an early developmental stage (E7.5, late gastrulation) to investigate the onset of these phenotypes. Furthermore, we analyzed Trim71-KO and wildtype yolk sacs at E9.5 by scRNA-seq to gain insight into the changes in gene expression at the developmental stage when vascular defects have become apparent.
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Project description:Kilian2024 - Immune cell dynamics in Cue-Induced Extended Human Colitis Model
Single-cell technologies such as scRNA-seq and flow cytometry provide critical insights into immune cell behavior in inflammatory bowel disease (IBD). However, integrating these datasets into computational models for dynamic analysis remains challenging. Here, Kilian et al., (2024) developed a deterministic ODE-based model that incorporates these technologies to study immune cell population changes in murine colitis. The model parameters were optimized to fit experimental data, ensuring an accurate representation of immune cell behavior over time. It was then validated by comparing simulations with experimental data using Pearson’s correlation and further tested on independent datasets to confirm its robustness. Additionally, the model was applied to clinical bulk RNA-seq data from human IBD patients, providing valuable insights into immune system dynamics and potential therapeutic strategies.
Figure 4c, obtained from the simulation of human colitis model is highlighted here.
This model is described in the article:
Kilian, C., Ulrich, H., Zouboulis, V.A. et al. Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease. npj Syst Biol Appl 10, 69 (2024). https://doi.org/10.1038/s41540-024-00395-9
Abstract:
Single-cell-based methods such as flow cytometry or single-cell mRNA sequencing (scRNA-seq) allow deep molecular and cellular profiling of immunological processes. Despite their high throughput, however, these measurements represent only a snapshot in time. Here, we explore how longitudinal single-cell-based datasets can be used for deterministic ordinary differential equation (ODE)-based modelling to mechanistically describe immune dynamics. We derived longitudinal changes in cell numbers of colonic cell types during inflammatory bowel disease (IBD) from flow cytometry and scRNA-seq data of murine colitis using ODE-based models. Our mathematical model generalised well across different protocols and experimental techniques, and we hypothesised that the estimated model parameters reflect biological processes. We validated this prediction of cellular turnover rates with KI-67 staining and with gene expression information from the scRNA-seq data not used for model fitting. Finally, we tested the translational relevance of the mathematical model by deconvolution of longitudinal bulk mRNA-sequencing data from a cohort of human IBD patients treated with olamkicept. We found that neutrophil depletion may contribute to IBD patients entering remission. The predictive power of IBD deterministic modelling highlights its potential to advance our understanding of immune dynamics in health and disease.
This model was curated during the Hackathon hosted by BioMed X GmbH in 2024.
2025-03-07 | MODEL2502180001 | BioModels
Project description:Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken during the first 24 hours of development of Lytechinus variegatus (Lv). Developmental trajectories were constructed using Waddington-OT, a computational approach to "stitch" together developmental timepoints. Skeletogenic and primordial germ cell trajectories diverged early in cleavage. Ectodermal progenitors were distinct from other lineages by sixth cleavage, though a small percentage of ectoderm cells briefly co-expressed endoderm markers indicating an early ecto-endoderm cell state, likely in cells originating from the equatorial region of the egg. Endomesoderm cells originated at 6th cleavage also and this state persisted for more than two cleavages, then diverged into distinct endoderm and mesoderm fates asynchronously, with some cells retaining an intermediate specification status until gastrulation. 79 of 80 genes (99%) examined, and included in published developmental gene regulatory networks (dGRNs), are present in the Lv-scRNA-seq dataset, and expressed in the correct lineages in which the dGRN circuits operate.
2021-09-24 | GSE184538 | GEO
Project description:This study identified circRNA-1572, which is delivered by sperm into the oocyte during fertilization, whose downregulation resulted in developmental arrest and inhibition of ZGA during porcine embryogenesis. Moreover, we elucidated that sperm-derived circRNA-1572 competitively binds to bta-miR-2478-L-2 through a “sponge” mechanism to target and regulate cyclin B2 expression, thereby modulating the distribution of F-actin in early pig embryos, ensuring proper chromosome segregation during mitosis, and facilitating normal embryo cleavage, maternal RNA degradation (MRD), and ZGA.
2025-05-29 | GSE288540 | GEO
Project description:Human primordial germ cells (hPGCs), the precursors of sperm and eggs, originate in early postimplantation embryos. Since early human embryos cannot be investigated directly, we extended our recent in vitro model for hPGC fate, alongside direct analysis of early porcine embryos, which develop in a highly similar manner. Here we show that porcine PGCs (pPGCs) originate from the posterior pre-primitive streak epiblast in response to WNT and BMP-pSMAD signalling, followed by sequential induction of SOX17–BLIMP1 expression. This is reminiscent of our observations for the human in vitro counterpart. Mechanistic analysis in the culture model for hPGC specification and gastrulation shows that a balanced SOX17-BLIMP1 gene dosage is critical and sufficient for PGC specification; SOX17 subsequently induces definitive endoderm during gastrulation. We demonstrate that porcine embryos when combined with a tractable human model system can provide insights on early human development and mechanisms of early cell fate decisions.
2017-06-08 | GSE85378 | GEO