Abstract: The present invention discloses novel markers for cell types found in breastmilk. Moreover, genes associated with various stages of lactation are identified and in vitro alveolar-like organoid models derived from breastmilk cells are disclosed. Methods of screening modulating agents with the alveolar-like organoid model are also provided. Therapeutic targets for controlling differentiation, proliferation, maintenance and/or function of the cell types disclosed herein, as well as novel cell types and methods of quantitating, detecting and isolating the cell types are disclosed.

Abstract: The present invention relates to functionalized solid supports and methods of making functionalized solid supports. Methods for preparing a population of high quality functionalized solid supports for use in various nucleic acid analysis methods are provided. The invention also provides methods for validation and quality control of the functionalization steps.

Abstract: Disclosed here is a generally applicable framework that utilizes massively-parallel single-cell RNA-seq to compare cell types/states found in vivo to those of in vitro models. Furthermore, Applicants leverage identified discrepancies to improve model fidelity. Applicants uncover fundamental gene expression differences in lineage-defining genes between in vivo systems and in vitro systems. Using this information, molecular interventions are identified for rationally improving the physiological fidelity of the in vitro system. Applicants demonstrated functional (antimicrobial activity, niche support) improvements in Paneth cell physiology using the methods.