Journal: ACS Chemical Biology

Article Title: Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction

doi: 10.1021/acschembio.3c00431

Figure Lengend Snippet: Imaging protein:protein complexes in human cells, mouse proT cells, and FFPE human breast tissue sections. (A,B) Imaging β-catenin:E-cadherin target complex in A-431 cells expressing β-catenin and E-cadherin (panel A) or HeLa cells expressing N-cadherin instead of E-cadherin (panel B). (C,D) Imaging RUNX1:PU.1 target complex in Scid.adh.2C2 mouse proT cells retrovirally transduced with a PU.1-expressing vector (panel C) or an empty vector (panel D). (E,F) Imaging β-catenin:E-cadherin target complex in 5 μm FFPE human breast tissue sections from the same patient: normal (panel E) or invasive lobular carcinoma (panel F). All panels: confocal image; single optical section; 0.18 × 0.18 × 0.8 μm pixels (panels A–D) or 0.57 × 0.57 × 3.3 μm pixels (panels E,F). Signal-to-backround ratio for each row (mean ± SEM for representative regions of N = 3 replicate samples). See sections S2.2–S2.4 for additional data.

Article Snippet: HCR imaging of protein:protein complexes was performed in 5 μm FFPE normal human breast tissue sections (Acepix Biosciences, HuN-06-0027) and 5 μm FFPE invasive lobular carcinoma human breast tissue sections (Acepix Biosciences, HuC-06-0101) from the same patient using the protocol detailed in section S1.11 .

Techniques: Imaging, Expressing, Transduction, Plasmid Preparation

Journal: ACS Chemical Biology

Article Title: Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction

doi: 10.1021/acschembio.3c00431

Figure Lengend Snippet: qHCR imaging: relative quantitation of protein:protein complexes with subcellular resolution in an anatomical context. (A) Two-channel redundant detection of a protein:protein complex: each target protein is detected by an unlabeled primary antibody probe and two batches of secondary antibody probes that interact with orthogonal proximity probes to colocalize full HCR initiators that trigger orthogonal spectrally distinct HCR amplifiers (Ch1, Alexa546; Ch2, Alexa647). (B) Two-channel confocal images; single optical sections. Top: β-catenin:E-cadherin complex in A-431 cells (0.18 × 0.18 × 0.8 μm pixels). Bottom: β-catenin:E-cadherin complex in a 5 μm FFPE normal human breast tissue section (0.57 × 0.57 × 3.3 μm pixels). (C) High accuracy and precision for protein:protein relative quantitation in an anatomical context. Highly correlated normalized signal (Pearson correlation coefficient, r ) for subcellular voxels in the indicated regions in panel B. Top: 2.0 × 2.0 × 0.8 μm voxels. Bottom: 2.0 × 2.0 × 3.3 μm voxels. Accuracy: linearity with zero intercept. Precision: scatter around the line. See section S2.6 for additional data.

Article Snippet: HCR imaging of protein:protein complexes was performed in 5 μm FFPE normal human breast tissue sections (Acepix Biosciences, HuN-06-0027) and 5 μm FFPE invasive lobular carcinoma human breast tissue sections (Acepix Biosciences, HuC-06-0101) from the same patient using the protocol detailed in section S1.11 .

Techniques: Imaging, Quantitation Assay

Journal: Nature Communications

Article Title: Cooperative integration of spatially resolved multi-omics data with COSMOS

doi: 10.1038/s41467-024-55204-y

Figure Lengend Snippet: a Annotation of P56 mouse brain coronal sections from the Allen Brain Atlas. b Manual annotation of tissue from P22 mouse brain coronal sections in Zhang et al., overlaid on the image from a . c Comparison of domain segmentation results from five algorithms. Note that SpaMultiVAE was excluded as it is not designed for ATAC-RNA multi-omics data analysis. d Distribution of modality weights for RNA and ATAC in COSMOS analysis. e UMAP visualizations of integrated embeddings produced by SpatialGlue and COSMOS. f Pseudo-spatiotemporal maps (pSM) generated by SpatialGlue and COSMOS. ( g) Gene Ontology Biological Process (GOBP) analysis of genes associated with pseudo-time. h Gene expression profiles for the top 15 positive and 15 negative pSM-associated genes. i Spatial mapping of gene expressions for brain development genes negatively ( Nexn, Bcl11b, Mbp ) and positively ( Nfix, Mef2c, Cux2 ) correlated with pseudo-time, as identified by COSMOS. The full names of the abbreviations of brain regions are: nucleus accumbens (ACB), caudoputamen (CP), lateral ventricle (VL), genu of corpus callosum (ccg) and anterior commissure olfactory limb (aco). Source data are provided as a Source Data file.

Article Snippet: The reference of mouse brain ATAC-RNA data is obtained from a P56 mouse brain coronal section from Allen Mouse Brain Atlas (Allen Institute for Brain Science: https://mouse.brain-map.org/static/atlas ).

Techniques: Comparison, Biomarker Discovery, Produced, Generated, Gene Expression

Journal: Cerebral Cortex (New York, NY)

Article Title: A Layer-specific Corticofugal Input to the Mouse Superior Colliculus

doi: 10.1093/cercor/bhx161

Figure Lengend Snippet: Areal characterization of cortico-superior-collicular neurons. (a) Epifluorescence images show retrogradely labeled neurons in a series of slices containing the AC. Dashed yellow lines indicate areal boundaries between the dorsal, primary, and ventral AC. (b) Schematic from the Allen Institute for Brain Science coronal mouse atlas which was used to reference the boundaries between the cortical areas. (c) Continuing in series from panel a. (d) Continuing in series from panel b.

Article Snippet: Dashed yellow lines indicate areal boundaries between the dorsal, primary, and ventral AC. ( b ) Schematic from the Allen Institute for Brain Science coronal mouse atlas which was used to reference the boundaries between the cortical areas. ( c ) Continuing in series from panel a. ( d ) Continuing in series from panel b.

Techniques: Labeling