stereo-seq transcriptomics set for chip-on-a-slide  (Complete Genomics Inc)

Journal: bioRxiv

Article Title: YAP disrupts bile acid homeostasis to drive cancer-associated cachexia

doi: 10.64898/2026.02.01.702698

Figure Lengend Snippet: a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with BGI Stereo-seq technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.

Article Snippet: Frozen tissue blocks were stored at −80 °C and cryosectioned at 10 μm onto STOmics Stereo-seq chips (V1.1; BGI Research).

Techniques: Spatial Transcriptomics, Staining, Marker, Expressing, Derivative Assay, Immunofluorescence

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

Journal: Horticulture Research

Article Title: Uncovering the genetic architecture of pungency, carotenoids, and flavor in Capsicum chinense via TWAS-mGWAS integration and spatial transcriptomics

doi: 10.1093/hr/uhaf243

Figure Lengend Snippet: Spatially resolved transcriptomic analysis of two contrasting C. chinense accessions, PI 656271 and PI 660973, was performed using Stereo-seq on 5-day post-anthesis (5-dpa) fruits to investigate tissue-specific gene expression patterns. Panel A illustrates the application of spatial transcriptomics to map gene activity within intact fruit tissues. Panel B presents a Uniform Manifold Approximation and Projection (UMAP) plot of spatial transcriptomic spots, where each dot represents an individual spatial location, and colors indicate distinct transcriptional clusters across the fruit sections. Panels C and D display the differential spatial expression of AP2 (APETALA2) transcription factors and PPR (Pentatricopeptide Repeat) genes, respectively, within Modules 1 and 2—gene modules identified as highly spatially correlated and differentially expressed between the two accessions. These spatial expression profiles reveal zone-specific regulatory networks involved in the biosynthesis of capsaicinoids, carotenoids, and volatile metabolites, offering insights into the tissue-level transcriptional control of fruit quality traits in C. chinense .

Article Snippet: Stereo-seq transcriptomics was conducted using the BGI Stereo-seq kit (catalog 211ST114, STOmics), following the manufacturer’s instructions with minor modifications [ ].

Techniques: Gene Expression, Activity Assay, Expressing, Control