2025-03-19 MAR

Spatial Transcriptomics

This C4B session is organized around Dr. Oscar Ospina presentation at NCI/CBIIT "user-friendly analysis of spacial transcriptomics with spatial GE". Note the presentation is R-centric while the C4B angle is directed to the interoperable web stack, i.e. keep an eye on the data structures, the SDKs and the reference repositories (cell atlases?). The presentation takes place 10:00-11:00, which gives us 30 mins 9:30-10:00 to warm up, and another 30 mins after the presentation, 11:00-11:30, to compare notes on data, applications and some idea of what SDKs would be helpful for in-browser tooling.

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SpatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics

Oscar E Ospina, Christopher M Wilson, Alex C Soupir, Anders Berglund, Inna Smalley, Kenneth Y Tsai, Brooke L Fridley

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Register: https://datascience.cancer.gov/news-events/events/user-friendly-analysis-spatial-transcriptomics-spatialge .

Single-cell analysis: Analytical techniques that examine the molecular characteristics of individual cells – for example, measuring each cell’s gene activity or DNA mutations – rather than averaging-out signals across bulk tissues. Averaging-out signals mask the inherent heterogeneity present in tissues.

Dissecting Cellular Heterogeneity Using Single-Cell RNA Sequencing
Human Cell Atlas: https://data.humancellatlas.org/
1. New Cell Atlases Reveal Untold Variety in the Brain and Beyond
Single-cell genomic sequencing for early detection of cancer: https://pmc.ncbi.nlm.nih.gov/articles/PMC5502711/

Virtual Cell Project: Building a computational model of a whole, living cell.