ImmGen: gene expression and regulation in immune cells

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The Immunological Genome Project (ImmGen) is a collaborative group of immunology and computational biology laboratories who have performed in current grant period using a rigorous data generation and QC pipeline, a thorough dissection of gene expression and its regulation in >250 defined cell populations of the mouse immune system. These data were used to computationally define co-regulated gene modules and predict putative regulators. ImmGen data have become an important resource for the immunology community, with frequently consulted web and smartphone supports. The proposed continuation will harness the collective strengths of the ImmGen group. It will complete the existing compendium (missing or recently described populations, transcriptome changes upon cell migration). Consortium labs will analyze the response to a panel of molecular triggers (vaccination, adjuvants, gut microbes, super-antigens, TLR ligands, allergic challenge): are there responses in un-recognized target cells, how does transcriptional activation resonate secondarily system-wide? The profiling will also extend to non-coding mlRNAs and lincRNAs, and apply high-throughput RNA-sequencing to augment and refine the microarray data. In addition, we will build on our computational analyses of regulatory networks, validating and strengthening these predictions, and assessing their molecular underpinning. Chromatin immunoprecipitation detected by sequencing (ChlP-seq) will be used to relate the expression profiles to the underlying chromatin structure, loading with Pol-ll, and DNA methylation, in a set of 30 cell types already profiled in ImmGen. This will provide a unique perspective on chromatin/transcription relationships in primary cells in vivo. We will also collaborate with the international Knockout Mouse Project (KOMP) to analyze transcriptional changes and their immunological consequences in a panel of 200 KG animals. 50 of these will be chosen to target transcription factors (TFs) predicted to be essential nodes by our existing studies; in complement, the genomic locations of these TFs will be mapped by ChlP-seq by collaborators at Genentech. ImmGen data and meta-data serve a need in Immunology research and are widely used. This important resource will be maintained and curated, expanding the several browsing modes already in place to support more complex user queries and data requests, enriching the data presented and its connectivity. The smartphone/tablet information space will continue to be supported, enriching the content served locally or addressable through on-line queries.