Integrating Open Single-Cell Transcriptomic Data into the Undergraduate Neuroscience Classroom: A SEA-AD Lab Experience

Presentation Abstract:

Advances in neuroscience increasingly rely on large-scale, publicly available datasets, yet undergraduate curricula rarely provide students with hands-on experience exploring these resources. To address this gap, we developed a one-day laboratory activity for upper-level life science courses using the Seattle Alzheimer’s Disease (SEA-AD) Brain Cell Atlas and the Chan Zuckerberg CellxGene interface. This lab allows students to explore single-cell transcriptomic data from both healthy and Alzheimer’s disease brains, supporting data literacy, hypothesis-driven thinking, and familiarity with cutting-edge research tools. During the lab, students learn to navigate the SEA-AD database, query specific cell types, and compare gene expression through a differential expression analysis between normal and disease states. Students interpret their findings in the context of neurodegenerative disease mechanisms, enhancing their ability to connect molecular data with functional neuroscience concepts. In pilot implementations, students reported increased confidence in using open data, improved understanding of neurobiological diversity, and a deeper appreciation for translational research. This activity can be adapted to neurobiology, behavioral neuroscience, or molecular neuroscience courses and serves as a foundation for more advanced research experiences, including potential for Course-based Undergraduate Research Experiences (CUREs), where students generate and test their own hypotheses using SEA-AD data. Faculty attending this session will gain guidance on implementing this activity, as well as general practical strategies for integrating open neuroscience datasets into classroom laboratories.

Presenters:

Robert Calin-Jageman, Ph.D., Shveta Parekh, Ph.D.

Using the Aging, TBI and Dementia Dataset to deliver a CURE

Presentation Abstract:

The presenters will highlight the design and implementation of course-based undergraduate research experiences (CUREs) using the Aging, TBI, and Dementia dataset from the Allen Institute using a variety of approaches. One presenter will demonstrate how to use the CREATE method to help students critically read and process scientific papers related to the dataset. The second presenter will describe resources and scaffolded activities for a semester-long course to help students develop individual research projects from hypothesis creation to data analysis and presentation. The third presenter will showcase a “treasure hunt”-style CURE using RNAseq gene expression data patterns in memory-related brain regions, ultimately exploring novel hypotheses of Alzheimer’s Disease. Participants will learn strategies to overcome resource limitations, increase student engagement, and scaffold the development of a unique individual research experience using open access data.

Presenters:

William (Bill) Grisham, Dorothy Kozlowski Ph.D. , Shara Stough, Ph.D.

From Data to Decisions: Neuroethics in the Era of Open Science

Presentation Abstract:

As advances in neuroscience and the growth of open-access datasets reshape research practices, undergraduate students need opportunities to critically evaluate the scientific and ethical implications of open science. In this interactive session, participants will engage with a classroom-ready module in which students analyze metadata from real open datasets related to psychiatric conditions through structured prompts that support examination of the process of science and relationships between neuroscience and society. Attendees will experience the activity as learners while exploring implementation and adaptation strategies for diverse courses and contexts. Participants will receive ready-to-use instructional materials and will have the opportunity to contribute to ongoing refinement and evaluation of the module.

Presenters:

Nouran Amin, PhD, Christin Monroe, Ph.D., Aparna Shah, Ph.D.

Form Follows Function: Building Scalable, Data-Driven Neuroscience Modules for Every Classroom

Presentation Abstract:

This 90-minute session supports educators to construct personalized, viable prototypes of authentic data-driven exercises ready for immediate classroom deployment. These prototypes will mimic our exercises derived from the Allen Institute’s open-access morphological and electrophysiological Cell Types database. Using this data set, we engineered a suite of flexible modules anchored in Neuroscience Core Concepts to illuminate structure-function relationships across diverse collegiate settings. To calibrate these resources for varied institutional needs, our "Grid of Engagement" empowers educators to filter activities by specific constraints, including time on task and student conceptual maturity. The framework we engineered maintains pedagogical rigor through rubrics and success measures that enable consistent assessment and troubleshooting of implementation challenges while preserving alignment with core concept-derived learning outcomes.

Presenters:

Rachael Hannah Ph.D., Alexandra Nowlan, Ph.D., Lauren Rudolph, Ph.D.