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Multicellular organisms are composed of many different specialized cell types. Organ function and ultimately phenotypic traits are the result of the interplay of their heterogeneous cell populations. Knowledge about the heterogeneity of gene expression patterns and interplay of different cell types is of great importance to basic and clinical research, but is still limited due to a lack of the high-resolution analysis of genomes or transcriptomes from single cells. The recent introduction of novel single cell resolved measurement techniques enable the generation of comprehensive data on the level of single genomes and proteoms. These techniques are likely to revolutionize our understanding of the scale of genomic, epigenomic, and transcriptomic diversity that occurs during organ development, stress conditions, aging, oncogenesis and tumor progression. In this application we propose to establish a single cell genomic platform through the purchase of a C1 single cell auto prep system from Fluidigm. This new technology enables to rapidly isolate, process, and profile individual cells for genomic analysis. Several SNSF funded groups from three different departments at ETH (D-BIOL, D-HEST, D-CHAB) have a strong commitment to establish a single cell analytics technology platform at ETH Zurich to study cell-to-cell variability in gene expression in diverse biological systems ranging from cancer biology to metabolism and to make this technology available to the larger Zurich scientific community. ETH is uniquely positioned to support this single cell analytics approach through the integration with its three established central technology platforms, including the Flow Cytometry Unit, the Functional Genomics Center Zurich (FGCZ) and the ICT unit of Personalized Health Technology (NEXUS), which provides services to biomedical researchers in data management and analysis. A comprehensive workflow among these three platforms complemented by the C1 single cell auto prep system will facilitate users from ETH and the University of Zurich to analyze complex and diverse biological systems on the single cell levels using fluorescent activated cell soring, microfluidics, single cell RNA sequencing and bioinformatics analysis.