T2D of Multi-omics
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB28715 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Integrated multi-omics analysis
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Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.
2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress
Project description:Multi-omics molecular profiling was performed on post-radical prostatectomy material from a cohort of 132 patients with localized prostate adenocarcinoma. Unsupervised classification techniques were used to build a comprehensive classification of prostate tumours based on three molecular levels: DNA copy number, DNA methylation, and mRNA expression.
2018-07-09 | E-MTAB-6127 | biostudies-arrayexpress
Project description:Multi-omics molecular profiling was performed on post-radical prostatectomy material from a cohort of 132 patients with localized prostate adenocarcinoma. Unsupervised classification techniques were used to build a comprehensive classification of prostate tumours based on three molecular levels: DNA copy number, DNA methylation, and mRNA expression.
2018-06-24 | E-MTAB-6128 | biostudies-arrayexpress
Project description:Multi-omics molecular profiling was performed on post-radical prostatectomy material from a cohort of 132 patients with localized prostate adenocarcinoma. Unsupervised classification techniques were used to build a comprehensive classification of prostate tumours based on three molecular levels: DNA copy number, DNA methylation, and mRNA expression.
2018-06-24 | E-MTAB-6126 | biostudies-arrayexpress
Project description:Multi-omics molecular profiling was performed on post-radical prostatectomy material from a cohort of 132 patients with localized prostate adenocarcinoma. Unsupervised classification techniques were used to build a comprehensive classification of prostate tumours based on three molecular levels: DNA copy number, DNA methylation, and mRNA expression.
2018-06-24 | E-MTAB-6131 | biostudies-arrayexpress
Project description:ATAC-seq (assay for transposase-accessible chromatin followed by sequencing) is widely used to decode chromatin accessibility. Here we performed high-sensitive ATAC-seq in 9 human liver samples from normal and T2D donors, and identified a set of differentially accessible regions (DARs). DARs were overlapped with publicly available CREs databases and integrated with multi-omics data to identify candidates for further experimental validations. We identified 7 DARs that mark putative regulatory elements including a candidate enhancer for the ACOT1 gene that regulates the balance of acyl-CoA and free fatty acids in the cytoplasm. The relevance of ACOT1 regulation in T2D was supported by the analysis of transcriptomics and proteomics data in liver tissue. Conclusions: Our strategy that integrates chromatin accessibility with DNA binding and other types of omics provides novel insights towards the role of genetic regulation in complex multifactorial diseases such as T2D.
2021-09-03 | GSE173277 | GEO
Project description:Inferring in humans biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to M-^StranslateM-^T the results to humans. In this context, the Systems Biology Verification for Industrial Methodology for Process Verification in Research (SBV IMPROVER) initiative had run a Species Translation Challenge for the scientific community to explore and understand the limit of translatability from rodent to human using systems biology. Therefore, a multi-layer omics dataset was generated that comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, the generation, processing and quality control analysis of the multi-layer omics dataset. The datasets are accessible in public repositories could be leveraged for further translation studies.
2014-06-10 | E-MTAB-2091 | biostudies-arrayexpress
Project description:Multi-omics single-cell profiling of surface proteins, gene expression and lymphocyte immune receptors from hospitalised COVID-19 patient peripheral blood immune cells and healthy controls donors. Identification of the coordinated immune cell compositional and state changes in response to SARS-CoV-2 infection or LPS challenge, compared to healthy control immune cells.
2021-03-17 | E-MTAB-10026 | biostudies-arrayexpress
Project description:Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome
| PRJEB37924 | ENA