Overview
The Cohort
Five premenopausal donors total, split across two modalities.
This is a small but deeply profiled cohort — the strength is depth and resolution rather than numbers.
Spatial Transcriptomics Platform & Design
The platform was GeoMx DSP (NanoString), profiling >18,000 genes across the 257 ROIs. What makes this paper methodologically distinctive is the morphologically guided ROI selection strategy — rather than capturing random or grid-based regions, the team used:
- H&E histology of adjacent sections to identify 19 functionally defined local cell community types
- Immunofluorescent (IF) staining with markers including:
- DAZL (oocyte marker) — used to specifically capture and isolate oocyte-containing regions
- SMA (smooth muscle actin) — for theca/stromal regions
- CD68 — for macrophages/immune cells
- Antibody-guided subarea sampling — capturing DAZL+ (oocyte) and DAZL− (surrounding cells) subareas within the same ROI in paired fashion
This approach enabled isolation of transcriptional programs for oocytes, theca cells, granulosa cells, cortex, and medulla with unprecedented spatial specificity.
The 257 ROIs broke down across donors as:
- Donor 1: 74 ROIs → 6 clusters
- Donor 2: 165 ROIs → 9 clusters
ROI types represented all 19 predefined functional ovarian compartments including primordial follicles, primary/secondary/antral follicles, cumulus granulosa, mural granulosa, theca, cortical stroma, medullary stroma, and blood vessels.
scRNA-seq Data
21,198 cells from 3 donors, identifying:
- 4 major cell types
- 4 immune cell subtypes
Cell types profiled included granulosa cells, theca/stromal cells, endothelial cells, and immune cells — providing complementary resolution to the spatial data.