Journal: Cell Reports Methods

Article Title: Differential expression analysis in single-cell and spatial RNA-seq without model assumptions

doi: 10.1016/j.crmeth.2026.101383

Figure Lengend Snippet: Measured statistical weights of cells in E18 mouse brain GABAergic and glutamatergic neurons do not match assumptions of common DGE analysis models (A) Total transcript (UMI) counts per cell N i in a combined E18 mouse brain dataset from 10× Genomics (see ). Each data point represents an individual cell. (B) Weight distribution coefficient ( WDC ) for the statistical weight of different mRNA transcripts. Each point shows WDC Z for a gene Z calculated directly from the measured transcript counts as described in . Standard, unweighted averaging of transcript counts utilized in most DGE analysis models assumes WDC Z = 0. Utilization of aggregate counts in pseudo-bulk models assumes WDC Z = 1. Neither reflects the reality.

Article Snippet: Mouse E18 cortex cells (hippocampus and subventricular zone) , 10X Genomics , https://www.10xgenomics.com/datasets/10-k-mouse-e-18-combined-cortex-hippocampus-and-subventricular-zone-cells-dual-indexed-3-1-standard-4-0-0.

Techniques:

Journal: Cell Reports Methods

Article Title: Differential expression analysis in single-cell and spatial RNA-seq without model assumptions

doi: 10.1016/j.crmeth.2026.101383

Figure Lengend Snippet: Statistical weights of cells significantly affect the calculated log 2 (FC) and p values (A) Effects of the statistical weights on log 2 (FC) between glutamatergic vs. GABAergic neurons in E18 mouse brain (same as in A) plotted for 12,087 genes with at least 50 total counts in glutamatergic neurons. 7% of these genes (847) have different signs of log 2 (FC) for common and weighted averages. 17% of the latter (143) have the difference between the two log 2 (FC) values > 0.25 and 3% (29) have the difference larger than 0.5. (B) Scatterplots for the mean expression (bottom) and weighted mean expression (top) of these genes in GABAergic ( x axis) and glutamatergic ( y axis) neurons. (C) Effects of the statistical weights on p values for genes plotted in (A). The common (unweighted) t test was performed based on relative count rather than logarithmic normalization to avoid artifacts of the latter. Among the genes with at least 50 total counts in glutamatergic neurons, the weighted t test found 3,993 genes with p < 10 −4 (of which 6 were not found by the common t test with p < 0.05 and 845 were not found by the Seurat’s default Wilcoxon test with p < 0.05. The common t test found 3,747 genes with p < 10 −4 (of which 3 were not found by the weighted t test with p < 0.05). The Wilcoxon test found 8,045 genes with p < 10 −4 (of which 3,523 were not found by the weighted t test with p < 0.05), which is clearly inconsistent with the scatterplots for either mean expression or weighted mean expression.

Article Snippet: Mouse E18 cortex cells (hippocampus and subventricular zone) , 10X Genomics , https://www.10xgenomics.com/datasets/10-k-mouse-e-18-combined-cortex-hippocampus-and-subventricular-zone-cells-dual-indexed-3-1-standard-4-0-0.

Techniques: Expressing

Journal: Cell Reports Methods

Article Title: Differential expression analysis in single-cell and spatial RNA-seq without model assumptions

doi: 10.1016/j.crmeth.2026.101383

Figure Lengend Snippet: Weighted statistical testing reduces false-positive DGE in spRNA-seq (Visium HD assay) (A) Top: Proliferating chondrocytes were selected in 3 sections from the same E18.5 tibia; shaded areas show the selected regions in high resolution images of H&E-stained sections. Bottom: Zoomed images of the selected areas. Colored dots mark 8 × 8 μm 2 bins used for the analysis of gene expression, which passed quality control based on the following criteria: >20 features per bin, >100 counts other than Col1a1 or Col1a2 per bin, mitochondrial genes between 0.1% and 5% UMI, and Col2a1 > 5% UMI. The bin color represents the relative expression of Col2a1 ( n Col 2 a 1, i ×10,000). (B) DGE analysis performed with the weighted t test- χ 2 test combination and Seurat’s FindMarkers function for all 3 possible pairwise comparisons between the selected areas. Only genes detected in at least 10% of the bins were analyzed.

Article Snippet: Mouse E18 cortex cells (hippocampus and subventricular zone) , 10X Genomics , https://www.10xgenomics.com/datasets/10-k-mouse-e-18-combined-cortex-hippocampus-and-subventricular-zone-cells-dual-indexed-3-1-standard-4-0-0.

Techniques: HD Assay, Staining, Gene Expression, Control, Expressing