Journal: Cell reports

Article Title: Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator

doi: 10.1016/j.celrep.2020.107805

Figure Lengend Snippet: (A) Coronal image of ventral V-SVZ showing NOTUM, Nestin-CFP, and GFAP labeling. Nestin-CFP expression was detected using anti-GFP staining. Nestin-CFP reliably labels most ventricle-contacting cells, including NSCs and ependymal cells. Scale bars: 20 μm. (B) Whole-mount staining showing NOTUM labeling in ventricle-contacting cells (lateral wall). Cyan arrowhead, NOTUM + GFAP + cells; white, NOTUM − GFAP + cells; yellow, NOTUM + GFAP − cells. Scale bars: 20 μm. (C) Top: workflow for SCOPE-seq using optically barcoded mRNA capture beads. Following barcoded cDNA synthesis, optical demultiplexing identifies the barcode on each bead. Scale bar: 20 μm. Bottom: pseudotemporal ordering of V-SVZ neuronal lineage cells, and Notum marking the astrocyte-aNSC transition. Astrocyte, orange; aNSC, green; TAC, blue; NB, purple. (D) Average size of pseudotemporally ordered neuronal lineage cells and the fraction of Notum + cells in each pseudotime bin. Shading color corresponds to the stages of differentiation labeled in (C). (E) Gene signatures of NOTUM-bound cells showing significant enrichment in aNSC and TAC. (F) Box plot of GSEA data showing the enrichment or depletion of WNT signaling pathway in individual cells and the quantification of enrichment scores in each cluster (unpaired t test, p < 0.001).

Article Snippet: To test the enrichment of WNT signaling pathway (Gene Set M5493-Molecular Signatures Database, Broad Institute) in the SCOPE-seq dataset, we computed the expression of each gene in each cell as the z-scored log 2 (counts per million + 1) and produced a ranked list for each cell.

Techniques: Labeling, Expressing, Staining, cDNA Synthesis

Journal: Journal of Cancer

Article Title: A Model to Predict Prognosis of Renal Cell Clear Cell Carcinoma Based on 3 Angiogenesis-related Long Non-coding RNAs

doi: 10.7150/jca.94685

Figure Lengend Snippet: Identification of AR-lncRNAs. (A-D) Heatmaps and volcano plots showing the differentially expressed lncRNAs (A, B) or genes (C, D) between ccRCC tissues and paracancerous tissues in the TCGA. In the heatmap, the red parts represent upregulated lncRNAs/genes, and the blue parts represent downregulated lncRNAs/genes. In the volcano plot, the green dots represent downregulated lncRNAs/genes, the red dots represent upregulated lncRNAs/genes, and the black dots represent lncRNAs/genes with no differential expression (log2 |FC| > 1, p < 0.05). (E) Venn diagram illustrating 39 angiogenesis-related genes identified from the TCGA, HALLMARK and GSEA databases. (F) Forest plot showing the 9 prognostic differentially expressed sAR-lncRNAs according to univariate COX regression analysis. (G) LASSO regression analysis was carried out to identify 5 sAR-lncRNAs. (H) The optimal LASSO model was constructed with the best parameter (λ=0.03). (I) Forest plot showing the 3 prognostic differentially expressed sAR-lncRNAs according to multivariate COX regression analysis. AR-lncRNAs, angiogenesis-related lncRNAs; ccRCC, clear cell renal cell carcinoma; TCGA, The Cancer Genome Atlas; sAR-lncRNAs, survival AR-lncRNAs.

Article Snippet: Angiogenesis-related genes (ARGs) were extracted from The Molecular Signatures Database gene sets ANGIOGENESIS-M14493 and HALLMARK_ ANGIOGENESIS (http://www. broad institute. org/gsea/msigdb/index.Jsp).

Techniques: Quantitative Proteomics, Construct