Sequencing Core

Sequencing Core Summary The mission of the HIPC program at LJI is to use hypothesis-free approaches to define comprehensive molecular profiles of T cell subsets in the context of lung pathogens. The areas of interest cover an extremely wide spectrum of “omics” analysis including: (i) analysis of global gene expression (bulk and single-cell RNA-seq), (ii) analysis of T cell receptors high variable sequences repertoire by bulk or single-cell TCR-seq, (iii) analysis of changes in global epigenetics profiles (genome-wide enhancer profiles) using single-cell ATAC-seq, in T cell memory subsets from patients infected and/or vaccinated against, SARS-CoV-2, Mycobacterium tuberculosis (Mtb), and other lung pathogens. All these “omics” applications rely on standardized and well-validated high-throughput Next-Generation Sequencing (NGS) methods – a key service provided by this Core. The Sequencing Core will support all NGS activities for all the three projects involved in this program. This will be facilitated by the extensive genomics expertise of its personnel and the availability of cutting-edge technologies and automated platforms to generate highly reproducible and robust sequencing data from a large number of samples. Practically, the Sequencing Core will interface directly with all three Projects and provide a standardized and quality-controlled pipeline consisting of receiving samples, sorting cells, preparing RNA/DNA, preparing libraries for high-throughput NGS, and transferring the resulting data to the Data Management and Analysis Core for subsequent analysis.