Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1254294 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33304603.fastq.gz | Fastqsanger.gz | |||
| SRR33304604.fastq.gz | Fastqsanger.gz | |||
| SRR33304605.fastq.gz | Fastqsanger.gz | |||
| SRR33304606.fastq.gz | Fastqsanger.gz | |||
| SRR33304607.fastq.gz | Fastqsanger.gz |
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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:Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by describing interactions between transcription factors (TFs) and their gene targets. The Assay for Transposase Accessible Chromatin (ATAC)-seq, coupled with transcription-factor motif analysis, provides indirect evidence of chromatin binding for hundreds of TFs genome-wide. Here, we propose methods for TRN inference in a mammalian setting, using ATAC-seq data to influence gene expression modeling. We rigorously test our methods in the context of T Helper Cell Type 17 (Th17) differentiation, generating new ATAC-seq data to complement existing Th17 genomic resources (plentiful gene expression data, TF knock-outs and ChIP-seq experiments). In this resource-rich mammalian setting our extensive benchmarking provides quantitative, genome-scale evaluation of TRN inference combining ATAC-seq and RNA-seq data. We refine and extend our previous Th17 TRN, using our new TRN inference methods to integrate all Th17 data (gene expression, ATAC-seq, TF KO, ChIP-seq). We highlight new roles for individual TFs and groups of TFs (“TF-TF modules”) in Th17 gene regulation. Given the popularity of ATAC-seq (a widely adapted protocol with high resolution and low sample input requirements), we anticipate that application of our methods will improve TRN inference in new mammalian systems and be of particular use for rare, uncharacterized cell types.
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Project description:Genome-wide phylogenetic analysis of mulberry varieties using double digest RAD-seq
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Project description:RAD-seq revealed paleogeographic distribution shifts of Trigonobalanus verticillata across Indochina Peninsula and Malay Archipelago (PRJCA041353)
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Project description:RAD-seq reduced-genome sequencing of 200 S. cerevisiae strains for phylogenetic analysis
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Project description:RAD-seq reduced-genome sequencing of 262 S. cerevisiae strains for phylogenetic analysis
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Project description:Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) provides an accurate way to depict the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However bulk sequencing entangles information from different cell types and obscures cellular heterogeneity. Here, we develop and validate Cellformer, a novel deep learning method, that deconvolutes bulk ATAC-seq into cell type-specific expression across the whole genome. Cellformer enhances the bulk ATAC-seq resolution and allows an efficient cell type specific open chromatin profiling on large size cohorts at a low cost. Applied to 191 bulk samples from 3 brain regions, Cellformer identifies cell type-specific gene regulatory mechanisms and putative mediators involved in resilient to Alzheimer’s disease (RAD), an uncommon group of cognitively healthy individuals that harbor a high pathological load of Alzheimer’s disease (AD). Cell type-resolved chromatin profiling unveils cell type specific pathways and nominates potential epigenetic mediators underlying RAD that may illuminate therapeutic opportunities to limit the cognitive impact of this highly prevalent yet incurable disease. Cellformer has been made freely and publicly available to advance analysis of high-throughput bulk ATAC-seq in future investigations.
2023-07-20 | GSE226529 | GEO