Journal: Genome Biology

Article Title: ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq

doi: 10.1186/s13059-025-03900-3

Figure Lengend Snippet: Schematic workflow and bioinformatics analysis of the ST-FFPE-mIF whole solution. (1) FFPE tissue section was mounted on the chip and performed de-paraffinization (2) The section on the chip was subjected to antigen repair, blocking, antibody incubation, and mIF imaging. Before the 2nd round of mIF staining, antibodies from the 1 st round should be removal, and the epitope would be re-exposed. Then, the above mIF protocol should be repeated to generate another mIF image. Nine-colored mIF images were obtained accordingly (3) Permeabilization, in situ cDNA synthesis and collection were conducted after De-crosslink (4) cDNA amplification, library construction, and sequencing were performed according to manufacturer’s protocol to obtain Stereo-seq sequencing result (5) mIF images and spatially resolved gene expression was subjected to downstream spatial visualization and bioinformatics analyses including image processing and spatial multi-omics analysis to address scientific questions

Article Snippet: Post-fixation, the Stereo-seq chip was air-dried, and the tissue section was incubated in permeabilization buffer (Cat# 211SN114, STOmics) supplemented with 3 μL of Tetramethylene sulfone (Cat#A610163, Sangon Biotech) for 25 min at 37 °C.

Techniques: Blocking Assay, Incubation, Imaging, Staining, In Situ, cDNA Synthesis, Amplification, Sequencing, Gene Expression, Biomarker Discovery