Journal: Nature Communications

Article Title: Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples

doi: 10.1038/s41467-023-36071-5

Figure Lengend Snippet: Overview of spatially resolved transcriptomics samples and filtering settings used in pre-processing steps

Article Snippet: Based on this recent development, we propose a strategy for spatial analysis of FF tissue specimens with moderate/low RIN scores, that we name RNA-Rescue Spatial Transcriptomics (RRST).

Techniques:

Journal: Nature Communications

Article Title: Spatial single-cell atlas reveals regional variations in healthy and diseased human lung

doi: 10.1038/s41467-025-65704-0

Figure Lengend Snippet: A Experimental outline including the location of sample collection from donated healthy human lungs, and the methods used for the mRNA-based cell type mapping. 1—trachea, 2—proximal bronchi, 3a—bottom part of upper left lobe, 3b—top part of upper left lobe, 3c—bottom part of lower left lobe. HybISS Hybridization-based in situ sequencing, SCRINSHOT Single-Cell Resolution IN Situ Hybridization On Tissues, RRST RNA-Rescue Spatial Transcriptomics. B UMAP of cells after leiden clustering profiled with HybISS, colored by the assigned cell type (35 cell types presented). Gen general, adv adventitial, nan not annotated. C Heatmap of relative abundance of clustered cell types between locations demonstrating their frequency across the profiled regions. Similarity in cell type composition between three distal lung regions can be assessed by hierarchical clustering dendrogram on the left side. D Representative histological images from four biological replicates of an analysed trachea (donor 4) and a distal lung (donor 1) biopsies with hematoxyllin and eosin (H&E) staining (up) coupled to the maps of cell types identified by HybISS on top of nuclei (DAPI, white) in the same sections (down). Spots represent detected transcripts, colored according to the corresponding cell type of the cell they were assigned to. Colors as in Fig. 1B. Dashed lines indicate the approximate borders of histologic compartments. SMG submucosal gland, aw airway, alv alveolar region, bv blood vessel. Scale bar 200 µm. E Cell type neighborhood enrichment graph representing cell types as nodes, and edges indicating a positive neighborhood enrichment (>2) between cell types across the profiled sections. Suggested neighborhoods are shown as bubbles. Node colors as in Fig. 1B. Source data are provided as a Source Data file.

Article Snippet: HybISS Hybridization-based in situ sequencing, SCRINSHOT Single-Cell Resolution IN Situ Hybridization On Tissues, RRST RNA-Rescue Spatial Transcriptomics.

Techniques: Hybridization, In Situ, Sequencing, In Situ Hybridization, Staining