Ontology highlight
ABSTRACT:
PROVIDER: PRJNA589464 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Analysis of transcriptome in a strand-specific manner to further refine previous genome annotation; RNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi ompR regulon and identify novel ompR regulated transcripts.
2009-03-03 | E-TABM-644 | biostudies-arrayexpress
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:To refine the timeframe of liver regeneration initiation and investigate the temporal characteristics of metabolic reprogramming in the preparatory stage, we here established partial hepatectomy model and performed gene expression profiling analysis using data obtained from RNA-seq of regenerating livers at different time points.
2025-03-01 | GSE255995 | GEO
Project description:Muscles undergo developmental transitions in gene expression and alternative splicing that are necessary to refine sarcomere structure and contractility. CUG-BP and ETR-3-like (CELF) family RNA binding proteins are important regulators of RNA processing during myogenesis that are misregulated in diseases such as myotonic dystrophy (DM1). In this work we report a function for Bruno 1 (Bru1, Arrest), a CELF1/2 family homolog in Drosophila, during early muscle myogenesis as well as during later stages of sarcomere assembly and myofiber maturation. We identify an imbalance in growth in sarcomere length and width during later stages of development as the mechanism driving abnormal radial growth, myofibril fusion and the formation of hollow myofibrils in bru1 mutant muscle. Molecularly, we characterize a genome-wide transition from immature to mature sarcomere gene isoform expression in flight muscle development that is blocked in bru1 mutants. We performed whole proteome mass spectrometry in control and bru1 mutant muscle to identify changes to the proteome, and correlated these changes to gene expression and exon use gleaned from mRNA-Seq. Our results reveal the conserved nature of CELF function in regulating cytoskeletal dynamics in muscle development, and demonstrate that defective RNA processing due to misexpression of CELF proteins causes wide-reaching structural defects and progressive malfunction of affected muscles that cannot be rescued by late-stage gene replacement.
2024-03-08 | PXD043308 | Pride
Project description:We conducted the genome-wide mRNA expression profiling in parallel with miRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for miRNA regulators.
2014-07-15 | GSE59401 | GEO
Project description:Samples are from a screening experiment on 5 laboratory cultures of the coral endosymbiont: Symbiodiniaceae (Symbiodinium linuchae, Breviolum psygmophilum, Durusdinium trenchii, Effrenium voratum and Fugacium kawagutii). Samples are also from a thermal stress experiment (increased temperatures from 26 to 32 degrees C) carried out on Durusdinium trenchii and Cladocopium goreaui, two common coral endosymbionts on the Great Barrier Reef. All samples were collected on Markes Tenax TA thermal desorption tubes.
Lawson, C.A., Possell, M., Seymour, J.R., Raina, J.B. and Suggett, D.J., 2019. Coral endosymbionts (Symbiodiniaceae) emit species-specific volatilomes that shift when exposed to thermal stress. Scientific reports, 9(1), pp.1-11.
2019-10-08 | MSV000084436 | MassIVE