Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA276115 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1813910.fastq.gz | Fastqsanger.gz | |||
| SRR1813920.fastq.gz | Fastqsanger.gz | |||
| SRR1813930.fastq.gz | Fastqsanger.gz | |||
| SRR1813940.fastq.gz | Fastqsanger.gz | |||
| SRR1813911.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 41 |
Similar Datasets
Project description:mRNA and small RNA associated with Crohn's disease behavior [RNA-Seq]
| PRJNA276116 | ENA
Project description:mRNA and small RNA associated with Crohn's disease behavior [RNA-Seq]
2020-04-17 | E-GEOD-66207 | ExpressionAtlas
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:mRNA-seq raw data of 4 Crohn's disease and 4 control from colon tissue
2022-01-01 | GSE164871 | GEO
Project description:To investigate the intestinal epithelial cellular responses to interferon-gamma (IFNγ), bulk RNA sequencing (RNA-seq) was performed on human small intestinal organoids (enteroids, n = 10) with and without IFNγ treatment (100 pg/ml). The enteroids were derived from endoscopic biopsy samples obtained from patients with Crohn's disease (CD).
2025-03-15 | GSE290417 | GEO
Project description:Short title: Innate Gene/miRNA MDP-response in CD RNA-seq and small RNA-seq were used to identify the expression of gene and microRNA (miRNA) in monocytes from healthy controls and patients with Crohn's Disease (CD), with and without NOD2 (nucleotide-binding oligomerization domain-containing protein 2) single nucleotide polymorphisms (SNPs) after stimulation with muramyl dipeptide (MDP).
2017-02-15 | GSE69446 | GEO
Project description:<p>Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer-associated ncRNA transcripts (PCATs) by <i>ab initio</i> assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the polycomb repressive complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1-repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.</p>
| phs000443 | dbGaP
Project description:Transposable elements (TEs) are threats to genome stability and thus small RNA-mediated heterochromatinization suppresses the transcription of TEs. Paradoxically, transcription of non-coding RNA (ncRNA) from TEs is needed for the production of TE-targeting small RNAs and/or recruiting the silencing machinery to TEs. Hence, specialized RNA polymerase II (Pol II) transcription machinery is required for such unconventional transcription in different organisms. Indeed, the developmental stage-specific Mediator complex (Med)-associated proteins play essential roles in the ncRNA transcription from TE-related sequences in Tetrahymena. Yet it remains unknown how those Med-associated proteins are linked to the TE transcription by Pol II. Here, have found that Pol II is regulated by Emit3, a stage-specific, TFIIB-like protein specialized in TE transcription. Hence, to find out potential interactions, we did LC-MS/MS analysis for immunoprecipitation samples of Emit3 and the zinc-ribbon mutated Emit3.
2025-05-13 | PXD057568 | Pride
Project description:Phagocyte-Associated Pathobionts in Crohn's Disease
| PRJNA1111553 | ENA