Journal: Annals of Translational Medicine

Article Title: SOX2 amplification and chromosome 3 gain significantly impact prognosis in esophageal squamous cell carcinoma

doi: 10.21037/atm-20-1290

Figure Lengend Snippet: Gene copy number variation and SOX2 protein expression status in esophageal squamous cell carcinoma tissue assessed by fluorescence in-situ hybridization (1,000×) and immunohistochemistry (100×). (A) SOX2 disomy or low polysomy; (B) chromosome 3 gain with three or more green signals; (C) SOX2 amplification; (D) negative SOX2 expression; (E) low SOX2 expression; (F) high SOX2 expression.

Article Snippet: Briefly, a SOX2 target probe (red fluorescent signal) spanning the locus 3q26.33 and a green centromeric probe on chromosome 3 (Empire Genomics, New York, USA) were selected for hybridization.

Techniques: Expressing, Fluorescence, In Situ Hybridization, Immunohistochemistry, Amplification

Journal: Annals of Translational Medicine

Article Title: SOX2 amplification and chromosome 3 gain significantly impact prognosis in esophageal squamous cell carcinoma

doi: 10.21037/atm-20-1290

Figure Lengend Snippet: Associations between SOX2 status and patient characteristics

Article Snippet: Briefly, a SOX2 target probe (red fluorescent signal) spanning the locus 3q26.33 and a green centromeric probe on chromosome 3 (Empire Genomics, New York, USA) were selected for hybridization.

Techniques: Expressing

Journal: Annals of Translational Medicine

Article Title: SOX2 amplification and chromosome 3 gain significantly impact prognosis in esophageal squamous cell carcinoma

doi: 10.21037/atm-20-1290

Figure Lengend Snippet: Kaplan-Meier survival curves for disease-free survival (DFS, A) and overall survival (OS, B). A significantly shorter DFS or OS was observed in the SOX2 amplification group, while a significantly longer DFS or OS was observed in the chromosome 3 gain group, compared with the group with low polysomy or disomy.

Article Snippet: Briefly, a SOX2 target probe (red fluorescent signal) spanning the locus 3q26.33 and a green centromeric probe on chromosome 3 (Empire Genomics, New York, USA) were selected for hybridization.

Techniques: Amplification

Journal: Annals of Translational Medicine

Article Title: SOX2 amplification and chromosome 3 gain significantly impact prognosis in esophageal squamous cell carcinoma

doi: 10.21037/atm-20-1290

Figure Lengend Snippet: Univariate and multivariate analysis for disease-free survival (DFS) and overall survival (OS)

Article Snippet: Briefly, a SOX2 target probe (red fluorescent signal) spanning the locus 3q26.33 and a green centromeric probe on chromosome 3 (Empire Genomics, New York, USA) were selected for hybridization.

Techniques: Adjuvant, Amplification, Expressing

Journal: iScience

Article Title: Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma

doi: 10.1016/j.isci.2023.108096

Figure Lengend Snippet: A unique SOX2 + ALK mutant population detected during development (A) Left and Middle: UMAP indicating the distribution of WT cells (based on the scRNAseq of the J2 iPSCs for all 8 time-points) and ALK mutant cells (based on the scRNAseq of the NB05 iPSCs for all 4 time-points); Right: UMAP indicating the overlap between the sequenced time-points of both cell lines, annotated red for the ALK mutant cells and blue for WT cells (right). In the left and middle UMAPs, the population detected in ALK mutant cells only is highlighted with a dashed line. (B) Top: UMAPS showing expression levels of ALK and SOX2 as seen in the development of the WT cells; Bottom: Predicted expression along the lineage trajectory shown in the diffusion plot of Figure 5 A and along the pseudotime shown in Figure 5 B. (C) Key developmental markers of NCC ( SOX9 and TWIST1 ), SCP (i.e., SOX10 , PLP1 ), Bridging cells ( ASCL1 ), CPC (i.e., PENK, TH, CHGA ), SAP (i.e., ISL1 and STMN2 ) for the different developmental populations, shared with between both cell lines, and the unique population detected only in the ALK mutant cell line. (D) Heatmap showing the relative expression of known SOX2 target and associated genes for the populations identified in the UMAPS shown in Figures 5 A and . See also Figures S5 and .

Article Snippet: Rat anti-human SOX2 , Fisher Scientific , Cat#14981182; RRID: AB_11219471.

Techniques: Mutagenesis, Expressing, Diffusion-based Assay

Journal: iScience

Article Title: Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma

doi: 10.1016/j.isci.2023.108096

Figure Lengend Snippet: Expression of SOX2 target genes in the ALK mutant population UMAP showing the expression of SOX2 target genes POU3F2 , HES1 , HES5 and ID4 . See also Figure S7 for additional marker analysis.

Article Snippet: Rat anti-human SOX2 , Fisher Scientific , Cat#14981182; RRID: AB_11219471.

Techniques: Expressing, Mutagenesis, Marker

Journal: iScience

Article Title: Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma

doi: 10.1016/j.isci.2023.108096

Figure Lengend Snippet:

Article Snippet: Rat anti-human SOX2 , Fisher Scientific , Cat#14981182; RRID: AB_11219471.

Techniques: Recombinant, Saline, Derivative Assay, Staining, Amplification, Sequencing, Software, In Vivo