Af0db220-5884-409d-8382-11ec691812d2 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001007865 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Single-cell multi-omic profiling of healthy controls, asymptomatic and hosptial-admitted COVID19 patients recruited from Addenbrookes and Royal Papworth hospitals, in collaboration with the NIHR Cambridge Bioresource. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors. Samples are pooled, with 4 donors per pool. Germ-line genotypes are provided (VCF) to aid demultiplexing of single-cell and assignment to specific patient donor samples.
| EGAD00001007867 | EGA
Project description:Single-cell multi-omic profiling of healthy controls, asymptomatic and hosptial-admitted COVID19 patients recruited from Newcastle University hospitals. These data also include healthy control volunteers treated with IV-LPS as inflammatory controls. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors.
| EGAD00001007866 | EGA
Project description:This study profiles single-cell transcriptomes derived from human periodontal granulation tissue collected during routine periodontal surgery at Guy’s Hospital, King’s College London. Tissue was harvested following step 1 and step 2 periodontal treatment. Following dissociation and quality control, libraries were prepared using the 10x Genomics Chromium Single Cell 3’ kit and sequenced on an Nextseq 2000. The study aimed to elucidate cellular heterogeneity in periodontal lesions in otherwise healthy individuals.
2025-10-23 | GSE294615 | GEO
Project description:p130Cas is a polyvalent adapter protein essential for cardiovascular development, and with a key role in cell movement. In order to identify the pathways by which p130Cas exerts its biological functions in endothelial cells we mapped the p130Cas interactome and its dynamic changes in response to VEGF using high-resolution mass spectrometry and reconstruction of protein interaction (PPI) networks with the aid of multiple PPI databases. The work presented here was based on a collaboration between University College London and University College Dublin. Dr Ian Evans (first author) and Prof. Ian Zachary (lab head), can be contacted at: Centre for Cardiovascular Biology and Medicine, Division of Medicine The Rayne Building, University College London, London WC1E 6JJ, United Kingdom. Contact details for University College Dublin collaborators can be found below.
2017-01-02 | PXD003902 | Pride
Project description:p130Cas is a polyvalent adapter protein essential for cardiovascular development, and with a key role in cell movement. In order to identify the pathways by which p130Cas exerts its biological functions in endothelial cells we mapped the p130Cas interactome and its dynamic changes in response to VEGF using high-resolution mass spectrometry and reconstruction of protein interaction (PPI) networks with the aid of multiple PPI databases. The work presented here was based on a collaboration between University College London and University College Dublin. Dr Ian Evans (first author) and Prof. Ian Zachary (lab head), can be contacted at: Centre for Cardiovascular Biology and Medicine, Division of Medicine The Rayne Building, University College London, London WC1E 6JJ, United Kingdom. Contact details for University College Dublin collaborators can be found below.
2017-04-01 | MSV000080860 | MassIVE
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:Synthetic peptides are commonly used in biomedical science for many applications in basic and translational research. Here, we assembled a large dataset of synthetic peptides whose identity was validated using mass spectrometry. We analyzed the mass spectra and used them for method validation as well as the creation of ground truth datasets and cognate databases. Contact: Michele Mishto, Head of the research group Molecular Immunology at King’s College London and the Francis Crick Institute, London (UK). Email: michele.mishto@kcl.ac.uk,
2022-10-11 | PXD031812 | Pride
Project description:Single-nucleus RNA sequencing enables high-resolution profiling of complex tissues, but its high cost limits large-scale studies. Sample pooling with genetic demultiplexing is a scalable solution, yet comparative benchmarks are lacking. We benchmarked four widely used tools using variants from SNP arrays or extracted from matched bulk RNA-Seq. Performance, including accuracy, runtime, robustness, and scalability, was evaluated. Real-world application to 10x RNA-Seq from human and multi-species heart tissue demonstrates the tools' utility for demultiplexing and doublet removal.
2025-07-30 | GSE298266 | GEO
Project description:Single-nucleus RNA sequencing enables high-resolution profiling of complex tissues, but its high cost limits large-scale studies. Sample pooling with genetic demultiplexing is a scalable solution, yet comparative benchmarks are lacking. We benchmarked four widely used tools using variants from SNP arrays or extracted from matched bulk RNA-Seq. Performance, including accuracy, runtime, robustness, and scalability, was evaluated. Real-world application to 10x RNA-Seq from human and multi-species heart tissue demonstrates the tools' utility for demultiplexing and doublet removal.
2025-07-30 | GSE298265 | GEO
Project description:Compare transcriptomes of control and USH1B patient iPSC-derived retinal pigment epithelium (RPE) to elucidate disease mechanisms of Usher syndrome type IB (USH1B). USH1B patient fibroblasts were collected at Great Ormond Street Hospital (GOSH) and reprogrammed to iPSCs. Control and patient iPSCs differentiated in vitro to generate retinal pigment epithelium (RPE) and collected for RNA-seq at 24 week. Sequencing was performed at University College London (UCL) Genomics on a NovaSeq 6000 system. Data aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b.
2023-08-22 | E-MTAB-12165 | biostudies-arrayexpress