In this proposal six NIH-funded faculty from the Broad Institute of MIT and Harvard request to purchase a Nanostring nCounterTM Analysis System. Nanostring is a new technology for multiplex measurement of up to 550 genes in cell lysates from any organism. The technology offers exceptional accuracy, reproducibility, and dynamic range, permits measurement in small cell numbers (as few as 2000 mammalian cells per sample), with minimal preparation steps (no enzymatic reactions), a medium throughput of samples, and a potentially low cost. It is thus complementary to whole-genome mRNA profiling with microarrays and enables measurement of transcriptional signatures in large numbers of samples, as well as in rare cell populations and paraffin-embedded clinical samples. In particular, the faculty will use Nanostring's nCounterTM to carry out unprecedented studies to decipher regulatory networks in mammalian immune cells, re-programming in multiple mammalian cell lineages, the regulatory roles of large non-coding RNAs (lincRNAs), and the evolution of gene regulation in yeasts. Preliminary data using an instrument on loan from Nanostring demonstrated that this technology generates quantitative, highly reproducible data with small numbers of cells. The nCounter system will be operated and maintained in the Genetic Analysis Platform (GAP) of the Broad Institute, where it will be accessible to all the major and minor users, as well as to a wider community of researchers from MIT and Harvard. A staff member, who is the leader of the expression profiling team in GAP and has extraordinary expertise in expression profiling technologies, is already available to operate and maintain the system and to instruct new users. This new equipment will enable cutting-edge research efforts supported by major NIH grants, including the NIH PIONEER and Innovator awards and U01, U54 and P01 program projects. It will also provide new capabilities for signature-based profiling to a large community of trainees and researchers at the Broad Institute, Harvard and MIT. Finally, it will help establish general methodologies for the use of signature- based profiling technologies applicable in organisms from bacteria to humans.

Public Health Relevance

The proposed research addresses how systems of genes work together to carry out a function, and rather than investigating single genes, we will dissect entire networks of genes using an instrument that can track many genes at once in a very large number of samples. We will impact discovery in two ways: first, we will use it to define the circuits controlling gene regulation in cell differentiation and the immune response and to help us rationally select drug targets in autoimmune disease and cancer;second, our success would encourage similar studies in the biomedical community in organisms from bacteria to humans.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biomedical Research Support Shared Instrumentation Grants (S10)
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Special Emphasis Panel (ZRG1-GGG-A (30))
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Birken, Steven
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Broad Institute, Inc.
United States
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Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni et al. (2013) Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nat Biotechnol 31:342-9
Garber, Manuel; Yosef, Nir; Goren, Alon et al. (2012) A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell 47:810-22
Chevrier, Nicolas; Mertins, Philipp; Artyomov, Maxim N et al. (2011) Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell 147:853-67
Rabani, Michal; Levin, Joshua Z; Fan, Lin et al. (2011) Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 29:436-42
Amit, Ido; Garber, Manuel; Chevrier, Nicolas et al. (2009) Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326:257-63