TY - JOUR T1 - A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses JF - bioRxiv DO - 10.1101/2021.08.06.455429 SP - 2021.08.06.455429 AU - Sean M. Gross AU - Mark A. Dane AU - Rebecca L. Smith AU - Kaylyn Devlin AU - Ian McLean AU - Daniel Derrick AU - Caitlin Mills AU - Kartik Subramanian AU - Alexandra B. London AU - Denis Torre AU - Cemal Erdem AU - Nicholas Lyons AU - Ted Natoli AU - Sarah Pessa AU - Xiaodong Lu AU - James Mullahoo AU - Jonathan Li AU - Miriam Adam AU - Brook Wassie AU - Moqing Liu AU - David Kilburn AU - Tiera A. Liby AU - Elmar Bucher AU - Crystal Sanchez-Aguila AU - Kenneth Daily AU - Larsson Omberg AU - Yunguan Wang AU - Connor Jacobson AU - Clarence Yapp AU - Mirra Chung AU - Dusica Vidovic AU - Yiling Lu AU - Stephan Schurer AU - Albert Lee AU - Ajay Pillai AU - Aravind Subramanian AU - Malvina Papanastasiou AU - Ernest Fraenkel AU - Heidi S. Feiler AU - Gordon B. Mills AU - Jake Jaffe AU - Avi Ma’ayan AU - Marc R. Birtwistle AU - Peter K. Sorger AU - James E. Korkola AU - Joe W. Gray AU - Laura M. Heiser Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/08/07/2021.08.06.455429.abstract N2 - The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods (synapse.org/LINCS_MCF10A). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes.Competing Interest StatementG.B.M. SAB/Consultant: Abbvie, AstraZeneca, Chrysallis Biotechnology, GSK, Ellipses Pharma, ImmunoMET, Infinity, Ionis, Lilly, Medacorp, Nanonstring, PDX Pharmaceuticals, Signalchem Lifesciences, Symphogen, Tarveda, Turbine, Zentalis Pharmaceuticals. Stock/Options/Financial: Catena Pharmaceuticals, ImmunoMet, SignalChem, Tarveda, Turbine Licensed Technology: HRD assay to Myriad Genetics, DSP patents with Nanostring. ER -