236600df-19b7-4fac-81e5-4c031d3277b4 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001004367 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Single cell RNA-seq analysis of human skin.
| EGAD00010001620 | EGA
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:Bulk and single cell RNA-seq analysis of human keratinocyte and human skin
| EGAS00001002981 | EGA
Project description:<p>The role of sebaceous glands (SGs) in the early pathogenesis of hidradenitis suppurativa (HS) is undefined, with unclear causal relationship to inflammatory sequelae. The aim of this study was to determine whether SG aberrations constitute a primary pathogenic driver in early HS and elucidate the underlying mechanism. Histological study, single-cell RNA sequencing (scRNA-seq), and in vitro functional assays were employed. Clinical specimens included non-lesional skin, early lesional skin from patients diagnosed with Hurley I HS, and healthy controls. Human SZ95 sebocytes were used for mechanistic studies, including gene knockdown with lentivirus, bulk RNA sequencing, and liquid chromatography-tandem mass spectrometry based lipidomic analysis. </p><p>The size of SG was significantly reduced in HS patients. Development aberration and significant downregulation of tight junction signaling (e.g., TJP1, OCLN, CLDN1) in HS SGs were revealed by scRNA-seq, associated with compromised barrier integrity and early CD45+ immune cell infiltration. Knockdown of CLDN1 in human SZ95 sebocytes recapitulated these findings, inducing a robust pro-inflammatory response and a shift toward keratinocyte-like lineage accompanied by metabolic reprogramming, specifically overproduction of lysophosphatidylcholine (LPC). Exogenous LPC directly promoted proliferation and inflammatory cytokine secretion in HaCaT keratinocytes. Collectively, these findings reposition SGs as instigators in the early pathogenesis of HS.</p>
2025-12-28 | MTBLS13578 | MetaboLights
Project description:This dataset contains bulk RNA sequencing data from primary tumor biopsy samples of patients with prostate adenocarcinoma. TPM-normalized expression values are provided along with sample metadata. The data were generated to support transcriptomic profiling of human prostate tumors and are related to a companion single-cell RNA-seq dataset from the same cohort.
2025-11-19 | GSE297742 | GEO
Project description:Single cell RNA-seq of human breast skin cells
| PRJEB64504 | ENA
Project description:Single-cell RNA-seq of human liver samples
| PRJNA894458 | ENA
Project description:RNA-seq, ChIP-seq and single cell RNA-seq of human skin Langerhans cells
| PRJNA492925 | ENA
Project description:To explore the cellullar and molecular alteration of human psoriasis, we collected full-thickness skin from the lesion region of 3 patients and the similar region of 3 healthy donors, and submit for single cell RNA sequencing (scRNAseq) with 10x genomics (V3.1). The transcriptional landscape of human psoriasis whole skin provide a unique view of immuno-regulation among skin cell types. 1. "Single cell transcriptional zonation of human psoriasis skin identifies an alternative immunoregulatory axis",<Cell Death Dis.>, 2021 May 6;12(5):450. https://yz-studio.shinyapps.io/shinyapph5ad/ 2. "Integrative single-cell transcriptomic investigation unveils long non-coding RNAs associated with localized cellular inflammation in psoriasis" <Front Immunol>2023 Sep 26:14:1265517. Integrated dataset: 106,675 cells from 11 healthy human skin and 79,887 cells from 9 psoriatic human skin https://yz-studio.shinyapps.io/psoriaticskincellatlas2/
2021-04-26 | GSE162183 | GEO
Project description:Insight into the pathophysiology of inflammatory skin diseases, especially at the proteomic level, is severely hampered by the lack of adequate in situ data. Skin microdialysis samples from patients with atopic dermatitis (AD, n=6), psoriasis vulgaris (PSO, n=7) or prurigo nodularis (PN, n=6), as well as healthy controls (n=7) were subjected to proteomics and multiplex cytokine analysis. Single-cell RNA sequencing of skin biopsy specimens was used to identify the cellular origin of cytokines. Among the top 20 enriched GO annotations, NAD metabolic process, regulation of secretion by cell, and pyruvate metabolic process were elevated in microdialysates from lesional AD skin compared with both nonlesional skin and controls. The top 20 enriched KEGG pathways in these three groups overlapped almost completely. In contrast, nonlesional skin from patients with PSO or PN and control skin showed no overlap with lesional skin in this KEGG pathway analysis. Lesional skin from patients with PSO, but not AD or PN, showed significantly elevated protein levels of IL-22 and MCP-1 compared to nonlesional skin. IL-8 was elevated in lesional vs nonlesional AD and PSO skin, whereas IL-12p40 was higher only in lesional PSO skin. Integrated single-cell RNA-seq data revealed identical cellular sources of these cytokines in AD, PSO and PN. Based on microdialysate, proteomic data of lesional PSO and PN skin, but not lesional AD skin, differed significantly from those of nonlesional skin. IL-8, IL-22, MCP-1 and IL-12p40 might be suitable markers for minimally invasive molecular profiling.
2024-08-22 | PXD050245 | Pride