Journal: Cancer Cell

Article Title: Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer

doi: 10.1016/j.ccell.2022.11.001

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Article Snippet: Sequencing reads from 10x Genomics Visium libraries were aligned to the human transcriptome reference GRCh38-2020-A using 10x Genomics SpaceRanger (v.1.3.0) and exonic reads were used to produce mRNA count matrices for each sample.

Techniques: Recombinant, Multiplex Assay, Expressing, DNA Extraction, Sequencing, Software

Journal: Cell reports

Article Title: Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation.

doi: 10.1016/j.celrep.2025.115300

Figure Lengend Snippet: Figure 1. Spatially resolved transcriptomic profiling and unsupervised spatial domain detection in the human dentate gyrus across the postnatal lifespan (A) Experimental design for acquiring SRT data in the human dentate gyrus (DG) across four age groups (i): infant (0–2 years), teen (13–18 years), adult (30–50 years), and elderly (70+ years). (ii) Dissected tissue blocks were scored to isolate the DG and then (iii) mounted onto Visium slides (103 Genomics) and stained. (iv) On-slide cDNA synthesis, followed by library construction and sequencing, provided spatially resolved gene expression, illustrated by SNAP25. (B) Spots labeled by spatial cluster from Br1412. (C) Gene expression across clusters. Dots are sized by the proportion of spots with non-zero expression and colored by mean log2 normalized counts, centered, and scaled. CA3&4, cornu ammonis 3 and 4; CA1, cornu ammonis 1; GCL, granule cell layer; SGZ, subgranular zone; WM, white matter; SLM, stratum lacu- nosum-moleculare; ML, molecular layer; SR, stratum radiatum; SL, stratum lucidum; CP, choroid plexus. (D) Strategy for pseudo-bulking spots across all spatial domains from all donors. (E) Scatterplot of the first two principal components (PCs) after pseudo-bulking, excluding CP, labeled by domain (color) and age (shape).

Article Snippet: Tissue sections were then fixed in chilled methanol, and stained according to the Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocol (catalog no. CG000160 Rev C, 10x Genomics) or Visium Spatial Tissue Optimization User Guide (catalog no. CG000238 Rev C, 10x Genomics).

Techniques: Staining, cDNA Synthesis, Sequencing, Gene Expression, Labeling, Expressing