FMT datasets
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47909 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9697727_1.fastq.gz | Fastqsanger.gz | |||
| ERR9697727_2.fastq.gz | Fastqsanger.gz | |||
| ERR9707210_1.fastq.gz | Fastqsanger.gz | |||
| ERR9707210_2.fastq.gz | Fastqsanger.gz | |||
| ERR9709070_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:FMT from AOS treated mice rescue busulfan disrupted spleen
2022-11-03 | GSE160965 | GEO
Project description:Faecal microbiota transplant as treatment for recurrent Clostridioides difficile infection
| PRJEB30298 | ENA
Project description:The early detection of tissue and organ damage associated with autoimmune diseases (AID) has been identified as key to improve long-term survival, but non-invasive biomarkers are lacking. Elevated cell-free DNA (cfDNA) levels have been observed in AID and inflammatory bowel disease (IBD), prompting interest to use cfDNA as a potential non-invasive diagnostic and prognostic biomarker. Despite these known disease-related changes in concentration, it remains impossible to identify AID and IBD patients through cfDNA analysis alone. By using unsupervised clustering on large sets of shallow whole-genome sequencing (sWGS) cfDNA data, we uncover AID- and IBD-specific genome-wide patterns in plasma cfDNA in both the obstetric and general AID and IBD populations. Supervised learning of the genome-wide patterns allows AID prediction with 50% sensitivity at 95% specificity. Importantly, the method can identify pregnant women with AID during routine non-invasive prenatal screening. Since AID pregnancies have an increased risk of severe complications, early recognition or detection of new onset AID can redirect pregnancy management and limit potential adverse events. This method opens up new avenues for screening, diagnosis and monitoring of AID and IBD.
2022-09-14 | E-MTAB-11607 | biostudies-arrayexpress
Project description:Mitochondria are not only the powerhouses of the cell. They are also dynamic signaling hubs, playing a key role in cellular metabolism and adaptation. Proper mitochondrial function depends largely on the import of proteins encoded by the nucleus. Using RNA immunoprecipitation and proximity labeling (TurboID), we show that Arabidopsis thaliana FRIENDLY (FMT) protein specifically recognizes the mRNAs of several organellar-destined proteins, mostly mitochondrial, and is in close proximity to these proteins during their translation. Remarkably, when FMT is absent, its target mRNAs lose their correct cellular localization. Our TurboID approach also confirms the interaction between FMT and the Nascent polypeptide Associated Complex (NAC), a ribosome-associated platform involved in the maturation and sorting of nascent peptides. Taken together, these results suggest that FMT, through its interaction with NAC and the ribosome, is involved in the spatial regulation of translation in the cell. FMT itself is under tight cellular control. It is rapidly degraded under stress but is overproduced in specific conditions, such as germination, impacting mitochondrial activity. Since mitochondria act as signaling hubs, this regulation of FMT could help the cell to quickly adapt to changing environments.
2026-03-05 | PXD061930 | Pride
Project description:16S data from FMT trial for the treatment of recurrent Clostridium difficile infection
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