Publicly available large-scale cancer datasets allow for the systematic analysis of complex genomic alteration associations in tumorigenesis. Here, we present a protocol to quantify diverse interaction patterns between genomic alterations. We describe steps to prepare a binarized alteration matrix and analyze mutation-copy number alteration (CNA) associations, including pairwise, high-order, and context-dependent associations. This protocol enables the analysis of context-specific genetic interactions. For complete details on the use and execution of this protocol, please refer to Maqueda-Real et al.1.

Induced pluripotent stem cells (iPSCs) are emerging as a valuable system for modeling tissues and organs. Here, we describe a highly scalable protocol for the differentiation of iPSCs into retinal pigment epithelium (RPE), including a new step that makes it easier for researchers to obtain a high-purity culture. We also describe a cryopreservation technique for RPE progenitor cells to enable their storage. The use of cryopreserved cells allows a subsequent reduction in differentiation time compared to the full protocol.

SummaryTumor organoids provide physiologically relevant three-dimensional (3D) models that overcome the limitations of two-dimensional cultures in drug screening. Here, we present a protocol for generating compact and reproducible ovarian cancer organoids using SKOV-3 cells embedded in growth-factor-reduced Matrigel and dispensed onto a 384-pillar plate. We describe automated cell-matrix dispensing, calcein-AM viability staining, and high-content fluorescence imaging for IC50 analysis. This protocol enables scalable, standardized, and high-throughput drug screening with tumor organoids for quantitative drug efficacy evaluation.

SummaryThe rapidly evolving field of rodent behavior research led to the development of the IntelliCage, enabling observer-independent experiments with mice. Here, we present a detailed protocol for IntelliCage-based automated cognitive profiling of mice that navigates users through all experimental steps. In addition to instructions on how to prepare, execute, and analyze the experiment, we provide empirically informed recommendations and notes that may help new users plan robust and reproducible IntelliCage-based experiments.For complete details on the use and execution of this protocol, please refer to Gastaldi et al.1