Kai-Ping Su
Research Mentor(s): Jun Hee Lee
Mentor Department: Molecular & Integrative Physiology
Authors:
Session: Session 4 (1:00pm – 1:50pm)
Presentation Type: Poster 70
Abstract
The Seq Scope is a powerful protocol that uses spatial transcriptomics and single-cell imaging to unravel complex relationships between genes and their effects. With Seq Scope, the Lee Lab had done meaningful research on previously lesser-known genes, such as Sestrins, and their roles in the human body. Much of the Seq Scope analysis is done on mice, and hence mice tissue collection is paramount to Seq Scope’s success. Mice are provided with enrichment, 12-hour light cycle, and regular check-ups by ULAM vets to ensure optimal health. Tissue is collected at the outer part of the ear, placed in eppendorfs, and then refrigerated. Mice tissue, large in quantity and high in quality, enables the Seq Scope to accurately analyze the effects of various environmental stresses. Moreover, because mice are physiologically similar to humans, analysis on mice also deepens understandings of similar genes in the human body. After the tissues have been processed and the genotyping done, HNE (histological) images and gene expressions are aligned using historef, an open-sourced, python based software. Historef detects fiducial markers, which are concentric circles present in both images, and finds arrangements where such markers overlap most optimally. In a given pair of images, there exists between 10 to 50 such matches, and the best match is determined based on inspection. Historef often fails on its own because of incorrect image orientations and corrupted fiducial markers. In such cases, the images are adjusted and cropped manually using Photoshop. Alignment is important as it allows researchers to visualize the locations of gene expressions, and thereby make observations and inferences about the genes. The merged image can also be analyzed further, for example by removing pixels based on contrast, to generate mappings of specific genes.
