Project description:This report details the automation, benchmarking, and application of a strategy for transcriptomic, proteomic, and metabolomic analyses from a common sample. The approach, Sample Preparation for multi-Omics Technologies (SPOT), provides equivalent performance to typical individual omic preparation methods, but it greatly enhances throughput and minimizes the resources required for multi-omic experiments. SPOT was applied to a multi-omics time course experiment for zinc-treated HL60 cells.
Project description:Proteomics part of multi-omic analyses of the citramalate fermentation were undertaken to uncover the reasons for remarkable citramalate productivity in an engineered strain of E. coli.
Project description:WGS data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy
Project description:Skin homeostasis is guided by spatiotemporal regulation of gene expression, establishing each stage of keratinocyte differentiation. The current study presents transcriptomic and chromatin profiling for the proliferating (basal) and differentiated (suprabasal) cell populations derived from neonate mice (p0-p2) skin epidermis. This multi-omic approach will enable idenitification of cell specific epidermal cross-talk central to the equlibirum.
Project description:RNA-Seq data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy
Project description:With existing evidence showing the difference in miRNA expression levels between non-cancer and cancer groups, the investigators assume that levels of DNA methylation, RNA expression as well as protein concentration will also be dysregulated during disease progression. Combining the power of multi-omic cancer biomarkers, the investigators hypothesize that the sensitivity and specificity of MiRXES MCST can be significantly improved compared to existing multi-cancer diagnostic tests.
In this study, the investigators propose to develop and validate blood-based, multi-cancer screening tests through a multi-omics approach.
Project description:Most existing single-cell techniques can only make one type of molecular measurements. Although computational approaches have been developed to integrate single-cell datasets, their efficacy still needs to be determined with reference to authentic single-cell multi-omic profiles. To address this challenge, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmC2T-seq) and applied the approach to post-mortem human frontal cortex tissue. We developed a computational framework to evaluate the quality of finely defined cell types using multi-modal information and validated the efficacy of computational multi-omic integration methods. Correlation analysis in individual cells revealed gene groups showing distinct relations between methylation and expression. Integration of snmC2T-seq with other multi- and single- modal datasets enabled joint analyses of the methylome, chromatin accessibility, transcriptome, and chromatin architecture for 63 human cortical cell types. We reconstructed the regulatory lineage of these cortical cell types and found pronounced cell-type-specific enrichment of disease risks for neuropsychiatric traits, predicting causal cell types that can be targeted for treatment.
Project description:LYN kinase is a tyrosine kinase, that regulates cellular homeostasis in a context-specific manner. Our group could show, that its expression in the leukemic microenvironment of chronic lymphocytic leukemia contributes to disease progression (Nguyen PH et al.; Cancer Cell; 2016). To analyze the effect of LYN kinase on the leukemia supportive phenotype of the bone marrow stromal cell line HS-5, we generated single cell clones of LYN deficient stroma cells. These cells were analyzed in a Multi-Omic approach, including ATAC-Seq analysis of adapted epigenetic regulations.
