RT Journal Article
SR Electronic
T1 A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.06.455429
DO 10.1101/2021.08.06.455429
A1 Sean M. Gross
A1 Mark A. Dane
A1 Rebecca L. Smith
A1 Kaylyn Devlin
A1 Ian McLean
A1 Daniel Derrick
A1 Caitlin Mills
A1 Kartik Subramanian
A1 Alexandra B. London
A1 Denis Torre
A1 Cemal Erdem
A1 Nicholas Lyons
A1 Ted Natoli
A1 Sarah Pessa
A1 Xiaodong Lu
A1 James Mullahoo
A1 Jonathan Li
A1 Miriam Adam
A1 Brook Wassie
A1 Moqing Liu
A1 David Kilburn
A1 Tiera A. Liby
A1 Elmar Bucher
A1 Crystal Sanchez-Aguila
A1 Kenneth Daily
A1 Larsson Omberg
A1 Yunguan Wang
A1 Connor Jacobson
A1 Clarence Yapp
A1 Mirra Chung
A1 Dusica Vidovic
A1 Yiling Lu
A1 Stephan Schurer
A1 Albert Lee
A1 Ajay Pillai
A1 Aravind Subramanian
A1 Malvina Papanastasiou
A1 Ernest Fraenkel
A1 Heidi S. Feiler
A1 Gordon B. Mills
A1 Jake Jaffe
A1 Avi Ma’ayan
A1 Marc R. Birtwistle
A1 Peter K. Sorger
A1 James E. Korkola
A1 Joe W. Gray
A1 Laura M. Heiser
YR 2021
UL http://biorxiv.org/content/early/2021/08/07/2021.08.06.455429.abstract
AB 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.