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: After permeabilization, the FFPE Dimer mix (Cat#211SN114, STOmics) was added and incubated at room temperature for 40 min.

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

Journal: The Journal of Biological Chemistry

Article Title: Dihydroxyacetone decreases the dATP pool, inducing replication stress and genomic instability in BEAS-2B cells

doi: 10.1016/j.jbc.2025.110876

Figure Lengend Snippet: DHA exposure results in DNA lesions and protein carbonylation. A, relative DCFDA fluorescence intensities from BEAS-2B cells exposed to 7.5 mM DHA and 250 μM TBHP for 24 and 48 h, respectively. B, measurement of oxidative DNA lesions using oxRADD after exposure to 7.5 mM DHA for 24 and 48 h. Cells were also exposed to 25 μM methylglyoxal (MG) as a positive control. C, measurement of crosslink-type DNA lesions using T4PDG RADD after exposure to 7.5 mM DHA for 24 and 48 h. D, immunoblot of protein carbonylation in DHA-exposed BEAS-2B cells at 24 and 48 h. Quantification of protein carbonylation levels from the three biological repeats. Graphs are displayed as the mean fluorescence intensity ± SEM over three biological replicates. The statistical difference was analyzed by one-way ANOVA and Dunnett's post hoc test and displayed as follows: ∗ p < 0.05 and ∗∗∗∗ p < 0.0001. DCFDA, dichlorodihydrofluorescein diacetate; DHA, dihydroxyacetone; oxRADD, oxidative repair assisted damage detection; TBHP, tert-butyl hydrogen peroxide; T4PDG, T4 pyrimidine dimer glycosylase.

Article Snippet: For crosslinks (T4PDG, M0308; NEB), only T4 pyrimidine dimer glycosylase (T4PDG) and endo IV were used.

Techniques: Fluorescence, Positive Control, Western Blot