Journal: bioRxiv

Article Title: Single-cell transcriptomic atlas of mouse oocyte development from growth to ovulation

doi: 10.64898/2026.03.11.710939

Figure Lengend Snippet: a , UMAP of GCs, colored by seven GC subtypes (Progenitor, Preantral 1, Preantral 2, Mitotic 1, Mitotic 2, Antral Mural and Atretic). b , Feature plots of representative subtype markers on the UMAP. c , Monocle3 pseudotime trajectory inferred for GCs, with the principal graph overlaid and direction indicated from progenitor toward antral mural cells. d , Heatmap of representative genes showing coordinated expression changes along the progenitor-to-mural trajectory (expression shown as z-scores). e , Heatmap of Hallmark ssGSEA scores across granulosa subtypes (z-scored per gene set). f , H&E image of a Stereo-seq FF V1.3 mouse ovary section (6-8 weeks old), with representative regions (α–θ) indicated. Scale bar, 100 μm. g , Cell2location-based spatial mapping of GC subtypes at cell-bin resolution. h , Zoom-in views of representative regions (α, β, γ, and θ) showing H&E morphology and spatial expression of selected marker genes. Scale bar, 50 μm.

Article Snippet: Publicly available mouse ovary Stereo-seq Transcriptomics FF v1.3 demo data were obtained from the STOmics website ( https://www.stomics.tech/col1347 ).

Techniques: Expressing, Marker

Journal: bioRxiv

Article Title: Single-cell transcriptomic atlas of mouse oocyte development from growth to ovulation

doi: 10.64898/2026.03.11.710939

Figure Lengend Snippet: Spatial maps showing cell2location-predicted localization of each annotated cell subtype on the Stereo-seq FF V1.3 ovary section (6–8 weeks old), displayed separately by subtype. Scale bar, 100 μm

Article Snippet: Publicly available mouse ovary Stereo-seq Transcriptomics FF v1.3 demo data were obtained from the STOmics website ( https://www.stomics.tech/col1347 ).

Techniques:

Journal: bioRxiv

Article Title: Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization

doi: 10.64898/2025.12.02.691876

Figure Lengend Snippet: ( A ) Overview of study design, donor and sample quality and metadata, tissue sampling strategy, and adjacent-section workflows. ( B ) Stereo-seq dataset from an anterior basal ganglia section (donor case ID 2724): left, spatial map with cell-type assignments; right, UMAP embedding resolving 10 major cell classes from the same section. ( C ) MERFISH+ dataset from an adjacent anterior section. Left, spatial map with cell-type assignments; right, UMAP embedding resolving 10 major cell classes corresponding to Stereo-seq in ( B ). ( D–G , progressively greater magnification) Multi-scale Stereo-seq enlarged views of the boxed region in ( B ), illustrating the resolution span from centimeter-scale tissue anatomy to micron-scale detection of individual transcripts, with corresponding cell-type labels ( D, E ), cell-contour segmentation ( F ), and single-cell detail ( G ). ( H–K , progressively greater magnification) Multi-scale MERFISH+ enlarged views of the boxed region in ( C ), showing transcripts for selected genes (DRD1, DRD2, PENK, CCK, SST, CHAT, MBP) (color coded) and other genes (gray coded) that define cell-types at micron-scale resolution. See color keys at ( K ). Scale bars as indicated

Article Snippet: To fit the 2 cm × 3 cm Stereo-seq chips (STOmics/Complete Genomics, 111ST13231-CG), each large brain section was trimmed and/or subdivided within the cryostat to approximately 18 mm × 28 mm dimensions ( ).

Techniques: Sampling