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DAC SysMed

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Dr Thomas Ulas
t.ulas@uni-bonn.de

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This DAC controls 7 datasets

Dataset ID	Description	Technology	Samples
EGAD50000000457	We performed a dietary intervention study comparing western diet, traditional diet and the supplementation of fermented banana beverage in a cohort of 66 individuals (22 in each study arm).	Illumina NovaSeq 6000	219
EGAD50000000495	Immune memory is key to effective antimicrobial responses, but the impact of mRNA vaccines on this process is not fully understood. Our research shows that SARS-CoV-2 mRNA vaccines alter the epigenetic profile of human macrophages, specifically enhancing histone acetylation, which is linked to immune training. Significant epigenetic changes, along with increased cytokine release, require two vaccine doses. However, these effects diminish over time but can be restored with a booster dose six months later, maintaining a strong pro-inflammatory response.	Illumina NovaSeq 6000	40
EGAD50000000894	In this study we established a comprehensive workflow to collect multi-omics single-cell data using a commercially available micro-well based platform. This included whole transcriptome, cell surface markers (targeted sequencing-based cell surface proteomics), T cell specificities, adaptive immune receptor repertoire (AIRR) profiles and sample multiplexing. With this technique we identified novel paired T cell receptor sequences for three prominent human CMV epitopes. In addition, we review the ability of dCODE dextramers to detect antigenspecific T cells at low frequencies by estimating sensitivities and specificities when used as reagents for single-cell multi-omics.	Illumina NovaSeq 6000	12
EGAD50000000943	This dataset provides insight into the immune response in extrapulmonary tuberculosis (EPTB), using bulk RNA-seq data to analyze different disease severities. Hierarchical clustering identified three distinct levels of severity, revealing disease progression driven by interferon and IL-1β-mediated signaling. Additionally, the dataset helped develop a diagnostic gene expression signature for both EPTB and pulmonary TB.	Illumina NovaSeq 6000	50
EGAD50000001118	The dataset comprises single-cell RNA sequencing (scRNA-seq) data derived from around 60,000 PBMCs collected from donors across different severity groups of extrapulmonary tuberculosis (EPTB) and healthy controls (3 healthy, 3 mild, 3 intermediate, 3 severe). The data include both transcriptomic and surface protein expression profiles obtained using the BD Rhapsody Single-Cell Multiomics System. Libraries were prepared for whole transcriptome analysis (WTA), AbSeq, and sample tagging, with sequencing performed on a NovaSeq 6000 system.	Illumina NovaSeq 6000	2
EGAD50000001474	This dataset includes 1,518 single-cell transcriptomes obtained via index-sorted flow cytometry and FlashSeq (CITE-seq). It contains raw data files (FASTQ), expert gating annotations, and AI-inferred gating strategies generated by ConvexGating. The samples cover multiple immune cell types, including CD8+ TEMRAs and pDCs, and are accompanied by detailed metadata on marker panels and experimental conditions. The dataset enables benchmarking of automated gating methods and supports the optimization of marker selection for single-cell profiling.	Illumina NovaSeq 6000	1518
EGAD50000002889	This dataset includes processed data files (count matrices, index sort data, metadata), expert gating annotations, and AI-inferred gating strategies generated by ConvexGating. The samples cover multiple immune cell types, including CD8+ TEMRAs and pDCs, and are accompanied by detailed metadata on marker panels and experimental conditions. The dataset enables creation of a Seurat object and benchmarking of automated gating methods and supports the optimization of marker selection for single-cell profiling.	Illumina NovaSeq 6000	1518