chromium single cell multiome atac gene expression platform  (10X Genomics)

Journal: bioRxiv

Article Title: Decoding the pituitary gonadotrope regulatory architecture governing the preovulatory surge in vivo

doi: 10.1101/2025.11.18.689023

Figure Lengend Snippet: (A) Spherical representation of gonadotrope cell organisation, with pseudotime (θ axis, blue dashed line) and latent time (ϕ axis, red dashed line). Each gonadotrope cell’s pseudotime and latent time values were projected onto a circular space, and smoothed models were used to combine them into a single trajectory (solid black line). Individual cells are shown as coloured points by sampling stage: D2 10 am (blue), PE 10 am (green), PE 6 pm (red), and E 10 am (yellow). The projection of cells onto this periodic model defines a new time value, the “regulatory time,” capturing the cyclical progression of cellular states across the estrus cycle. (B) Ordering of pituitary gonadotrope cells according to pseudotime, latent time or regulatory time, with colours corresponding to the sampling stage. The upper panel shows the expected distribution according to the stage of sample collection. (C-E) Heatmaps of DAEs ( C ), GDVs ( D ) and DEGs ( E ) in gonadotrope cells across regulatory time. The upper panel shows gonadotrope cell distribution according to regulatory time. Signals are shown for each region or gene (lines) across the regulatory time (columns). The heatmap colour scale represents the relative signal (Z-score) in gonadotrope cells across the regulatory time. DAEs, GDVs and DEGs are clustered based on their respective accessibility (Cluster A1 to A5), velocity (Cluster V1 to V5) or expression profiles (Cluster E1 to E4). A dotted line indicates the transition between early to late PE, framing the preovulatory surge. (F) Identification of differentially regulated genes in gonadotrope cells across the estrus cycle. A gene was considered differentially regulated if associated with a DAE and displaying differential velocity and expression across regulatory time. The Venn diagram represents the overlap between GDV, DEG and DAE-associated genes. (G) Mean temporal trajectories of chromatin accessibility, mRNA velocity and mRNA abundance for each identified pair of gene and DAE (n = 1816 pairs). Mean ± SEM signals are plotted across the regulatory time. ATAC and RNA data are rescaled to a common amplitude (left y-axis) for comparison, while velocity is shown on its native scale (right y-axis).

Article Snippet: Nuclei purified from frozen hemi-pituitaries collected in the four above-mentioned females were processed using the Single Cell Multiome ATAC + Gene Expression platform (10x Genomics), followed by high-throughput sequencing.

Techniques: Sampling, Expressing, Comparison