Journal: PLoS ONE

Article Title: Long non-coding RNA Peg13 attenuates the sevoflurane toxicity against neural stem cells by sponging microRNA-128-3p to preserve Sox13 expression

doi: 10.1371/journal.pone.0243644

Figure Lengend Snippet: A. Pathway analysis indicated that the Sox13-related signal pathways were involved in the sevoflurane-related neurotoxicity in NSCs. B, C. Western blotting displayed that sevoflurane exposure decreased Sox13 expression in NSCs. D. Bioinformatics predicted that miR-128-3p bound to the 3′UTR of Sox mRNA. E. Luciferase reporter assay indicated that miR-128-3p over-expression reduced the wild-type Sox13-regulated, but not its mutant-regulated, luciferase expression in 293T cells. F, G. Peg13 over-expression restored Sox13 expression in the sevoflurane-exposed NSCs, which was mitigated by miR-128-3p over-expression. H. A diagram illustrates the mechanisms underlying the regulatory role of the Peg13/miR-128-3p/Sox13 axis in sevoflurane-related neurotoxicity in NSCs. Data are representative images, or expressed as the mean ± SEM of each group of cells from three separate experiments. * P <0.05, ** P <0.01, *** P <0.001, determined by Student T test or ANOVA.

Article Snippet: The membranes were blocked with 5% skim milk in TBST, and incubated with primary antibodies against Sox13 (1:1000, Santa Cruz Biotechnology, CA, USA) and β-actin (1:1000, Cell Signaling Technology) at 4°C overnight.

Techniques: Western Blot, Expressing, Luciferase, Reporter Assay, Over Expression, Mutagenesis

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: Validation of SOX13 flow sensitivity in ECs. (A) Violin plot shows SOX13 expression profile in our published scRNAseq data obtained from the mouse LCAs and RCAs at the 2-day (acute) or 2 weeks (chronic) post-PCL (partial carotid ligation) surgery. E2 represents a healthy EC cluster exposed to s-flow in RCA. E5 and E8 are EC clusters exposed to acute and chronic d-flow, respectively. (B) Chromatin accessibility plot of Sox13 gene was obtained by re-analyzing the published scATACseq data using the same mouse PCL model. E2 (s-flow), E5 (acute d-flow), and E8 (chronic d-flow) show a time-dependent closure of SOX13 accessibility by d-flow in ECs. (C–E) HAECs exposed to ULS or OSS for 24 h were lysed, fractionated into the cytoplasmic (cyto) and nuclear (nuc) fractionations, and western blot analyzed using antibodies to SOX13, laminA/C, and α-tubulin (C) and quantified (D) . Mean±SEM, n = 5, p -values calculated by student’s t -test. (E) Shows SOX13 qPCR from a similar HAEC shear study, Mean±SEM, n = 8, p -values calculated by student’s t -test. (F) Shows immunofluorescence staining of Sox13 of mouse GC (greater curvature exposed to stable flow) and LC (lesser curvature exposed to disturbed flow) naturally in the aortic arch. The bottom panels show orthogonal views, showing SOX13 expression above the internal elastic lamina (IEL). DAPI shows nuclei. (G) Shows the quantitation of SOX13 expression. Mean±SEM, n = 3 mice, p ≤ 0.05 by student’s t -test.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques: Expressing, Ligation, Western Blot, Immunofluorescence, Staining, Quantitation Assay

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: siSOX13 knockdown of SOX13 in HAECs. (A–C) Static HAEC study. HAECs were treated with siSOX13 vs. siCtrl for 48 h, and analyzed by qPCR (A) and western blot using cytoplasmic and nuclear fractions with SOX13 antibody (B) and quantified (C) . (D–L) Shear study. HAECs treated with siSOX13 vs. siCtrl for 48 h were exposed to ULS or OSS for another 24 h, and analyzed for SOX13 by qPCR (D) , western blot of whole cell lysate (E,F) . Additional qPCR assays for VCAM1 , KLF4 , and KLF2 (G–I) and western blots for VCAM1 and KLF4 (J,L) were conducted. Mean±SEM, n = 4–6 (F,I) or 3 (K,L) are shown, and p -values calculated by student’s t -test.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques: Western Blot

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: Shear-dependent and SOX13-dependent gene expression in HAECs by RNAseq analysis. HAECs treated with siSOX13 or siCtrl for 24 h were exposed to OSS or ULS for another 24 h, and total RNAs were analyzed by RNAseq. (A–D) Shows differential gene expression by comparing the four groups: (1) siCtrl OSS, (2) siSOX13 OSS, (3) siCtrl LSS, and (4) siSOX13 LSS. The number of significantly downregulated (left) or upregulated (right) genes by ≥50% with a p -value ≤ 0.05 (shown as red dots) are indicated in each volcano plot. (E,F) Venn diagrams show commonly downregulated genes by OSS or siSOX13 (E) and upregulated genes by OSS or siSOX13 in ULS condition (F) . (G,H) Heat map of the 94 commonly downregulated genes by OSS or siSOX13 in ULS condition (G) and the 40 commonly upregulated by OSS or by siSOX13. (I) Heatmap of top 20 genes upregulated by siSOX13 regardless of shear conditions.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques: Expressing

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: Gene ontology analysis of shear-dependent and SOX13-dependent genes. Biological processes enriched by the 94 commonly downregulated genes by OSS or siSOX13 in ULS condition (A) , the 40 commonly upregulated by OSS or by siSOX13 (B) , and the top 20 genes upregulated by siSOX13 regardless of shear conditions (C) are shown. All biological processes listed were significant by p -value.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques:

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: Validation of SOX13 targets by qPCR and ELISA. HAECs treated with siSOX13 or siCtrl for 24 h were exposed to OSS or ULS for another 24 h, and total RNAs were analyzed by RNAseq to validate the top SOX13-dependent targets (A) n = 4–7, Mean±SEM are shown. * p ≤ 0.05, ** p ≤ 0.01 *** p ≤ 0.001, and **** p ≤ 0.0001 as determined by student’s t -test. The conditioned media from HAECs treated with siSOX13 and shear (B,D) or static (C,E) conditions were analyzed by ELISA quantification of CCL5 (B,C) or CCL10 (D,E) . Mean±SEM are shown, p -values determined by student’s t -test.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques: Enzyme-linked Immunosorbent Assay

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: SOX13 plasmid overexpression reduces inflammatory markers and chemokine expression. (A) Western blot of whole cell lysate and (B) qPCR of SOX13 plasmid concentration curve in static HAECs after 48h compared to GFP control plasmid. (C) qPCR analysis of SOX13 targets following 48 h static SOX13 or GFP control overexpression in HAECs at a concentration of 200 ng, using SOX13 and AQP1 as positive controls. n = 3, Mean±SEM are shown. * p ≤ 0.05, ** p ≤ 0.01 as determined by student’s t -test. (D) ELISA quantification of CCL5 and (E) CXCL10 in the conditioned media from static HAECs, 48 h following SOX13 or control plasmid transfection. Mean±SEM are shown, n = 3, p -values determined by student’s t -test.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques: Plasmid Preparation, Over Expression, Expressing, Western Blot, Concentration Assay, Enzyme-linked Immunosorbent Assay, Transfection

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: Monocyte adhesion induced by siSOX13 is prevented by treating HAECs with MetCCL5. (A) HAECs overexpressing SOX13 or RFP control were exposed to OSS or ULS for another 24 h. Following shear, THP1 monocytes were added to the conditioned media (CM), and adhered monocytes were counted. (B) HAECs treated with siSOX13 or siCtrl were exposed to OSS or ULS for another 24 h. Following shear, THP1 monocytes were added to the CM, and adhered monocytes were counted. (C,D) HAECs treated with siSOX13 or siCtrl were exposed to OSS or ULS in the presence or absence of MetCCL5 for another 24 h. Following shear, THP1 monocytes were added to the CM, and adhered monocytes were counted (C) . In panel (D) , following shear, CM was removed, HAECs were washed with fresh medium, THP1 monocytes were added to the CM, and adhered monocytes were counted. Mean±SEM are shown, n = 3 to 7, p -values determined by one-way ANOVA.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques:

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: Mouse qPCR primer sequences.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques:

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: Human qPCR primer sequences.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques:

Journal: Frontiers in Cardiovascular Medicine

Article Title: Sox13 is a novel flow-sensitive transcription factor that prevents inflammation by repressing chemokine expression in endothelial cells

doi: 10.3389/fcvm.2022.979745

Figure Lengend Snippet: Antibodies used for western blotting and immunostaining.

Article Snippet: SOX13-myc-DDK-tagged (Origene RC210697) was used with a GFP- or RFP-(for monocyte adhesion assay) expressing plasmid with the same backbone as a control (pCMV backbone from Addgene #11153).

Techniques: Western Blot, Immunostaining

Journal: Brain

Article Title: POU3F2 regulates canonical Wnt signalling via SOX13 and ADNP to expand the neural progenitor population

doi: 10.1093/brain/awaf221

Figure Lengend Snippet: POU3F2 activates expression of SOX13 and ADNP to regulate canonical Wnt signalling in NPCs. ( A ) Potential direct effectors of POU3F2 were prioritized if they belonged to the TCF-dependent signalling in response to Wnt Reactome pathway (R-HSA-201681). ( B ) Quantification of ADNP protein expression measured via western blotting in POU3F2 WT and POU3F2 MUT NPCs, mean ± SEM ( n = 4 differentiations). Paired t -test, * P < 0.05. ( C ) Quantification of SOX13 protein expression measured via western blotting in POU3F2 WT and POU3F2 MUT NPCs, mean ± SEM ( n = 5 differentiations). Paired t -test, ** P < 0.01. ( D ) Schematic of experimental design for overexpression of a gene of interest followed by the SUPERTOPFLASH canonical Wnt reporter assay. ( E ) Baseline canonical Wnt signalling, as measured by a SUPERTOPFLASH assay, in POU3F2 WT and POU3F2 MUT NPCs expressing GFP (negative control) or ADNP, mean ± SEM ( n = 3 differentiations). Mixed-effects model with post hoc Sidak's test, ns = not significant. ( F ) Activated canonical Wnt signalling, as measured by a SUPERTOPFLASH assay, in POU3F2 WT and POU3F2 MUT NPCs expressing GFP (negative control) or ADNP, mean ± SEM ( n = 3 differentiations). Mixed-effects model with post hoc Sidak's test, * P < 0.05, ** P < 0.01. ( G ) Baseline canonical Wnt signalling, as measured by a SUPERTOPFLASH assay, in POU3F2 WT and POU3F2 MUT NPCs expressing GFP (negative control) or SOX13, mean ± SEM ( n = 3 differentiations). GFP control data represented here is included in . Mixed-effects model with post hoc Sidak's test, * P < 0.05, ** P < 0.01. ( H ) Activated canonical Wnt signalling, as measured by a SUPERTOPFLASH assay, in POU3F2 WT and POU3F2 MUT NPCs expressing GFP (negative control) or SOX13, mean ± SEM ( n = 3 differentiations). GFP control data represented here is included in . Mixed-effects model with post hoc Sidak's test, * P < 0.05, *** P < 0.001. ( I ) Genomic structure of SOX13 . Box above gene indicates relative position of gRNA target sequence. Western blot validation of SOX13 knockdown (GAPDH = loading control). ( J ) Gene ontology pathway enrichment results of differential gene expression in SOX13 MUT NPCs, separated by directionality of log 2 fold change. ( K ) GSEA of Wnt-activated targets and G2/M progenitor markers in SOX13 MUT versus SOX13 WT differential expression. ( L ) Model of POU3F2-mediated regulation of canonical Wnt signalling and progenitor expansion via transcription of ADNP and SOX13 . Schematics created in BioRender. Benoit, C. (2025) https://BioRender.com/35q22ly , https://BioRender.com/baxexcu . gRNA = guide RNA; GSEA = gene set enrichment analysis; MUT = mutant; NPC = neural progenitor cell; SEM = standard error of the mean; WT = wild-type.

Article Snippet: Primary antibodies diluted in blocking buffer were applied overnight at 4°C: POU3F2 (CST, Cat. No. 12137S, 1:1000), GAPDH (Proteintech, Cat. No. 60004-1-Ig, 1:10 000), β-catenin (CST, Cat. No. 8480S, 1:1000), Nestin (Novus Biologicals, Cat. No. MAB1259, 1:1000), TUJ1 (Novus Biologicals, Cat. No. NB100-1612, 1:1000), POU3F2 (Santa Cruz, Cat. No. sc-393324, 1:1000), HA-Tag (CST, Cat. No. C29F4, 1:500), ADNP (Abcam, Cat. No. ab300114, 1:500), SOX13 (Proteintech, Cat. No. 18902-1, 1:1000).

Techniques: Expressing, Western Blot, Over Expression, Reporter Assay, Negative Control, Control, Sequencing, Biomarker Discovery, Knockdown, Gene Expression, Quantitative Proteomics, Mutagenesis

Journal: Journal of Oncology

Article Title: Genomic Profiling and Functional Analysis of let-7c miRNA-mRNA Interactions Identify SOX13 to Be Involved in Invasion and Progression of Pancreatic Cancer

doi: 10.1155/2020/2951921

Figure Lengend Snippet: Putative target genes of let-7c using anticorrelation mRNA gene signature.

Article Snippet: For target gene knockdown functional experiments, predesigned pool of 3 target-specific 19–25 nt siRNAs designed to knock down SOX13 gene expression (Santa Cruz Biotech., sc-38424), a control (nontransfected), and a scrambled control siRNA (sc-37007) were used.

Techniques: In Silico

Journal: Journal of Oncology

Article Title: Genomic Profiling and Functional Analysis of let-7c miRNA-mRNA Interactions Identify SOX13 to Be Involved in Invasion and Progression of Pancreatic Cancer

doi: 10.1155/2020/2951921

Figure Lengend Snippet: (a) Expression of miR-let-7c potential gene target SOX13 in adjacent normal pancreas and PDAC tumour tissue. (b) SOX13 mRNA significantly higher in TCGA pancreatic tumour compared with normal tissue. (c) Kaplan–Meier overall survival of TCGA pancreatic cancer patient's cut-off into low vs. high SOX13 mRNA expression. (d) Kaplan–Meier overall survival of independent cohort of pancreatic cancer patients dichotomized into negative vs. positive SOX13 protein expression by IHC.

Article Snippet: For target gene knockdown functional experiments, predesigned pool of 3 target-specific 19–25 nt siRNAs designed to knock down SOX13 gene expression (Santa Cruz Biotech., sc-38424), a control (nontransfected), and a scrambled control siRNA (sc-37007) were used.

Techniques: Expressing

Journal: Journal of Oncology

Article Title: Genomic Profiling and Functional Analysis of let-7c miRNA-mRNA Interactions Identify SOX13 to Be Involved in Invasion and Progression of Pancreatic Cancer

doi: 10.1155/2020/2951921

Figure Lengend Snippet: Immunohistochemistry of independent pancreatic cancer cohort stained for SOX13 . Representative images show (a) negative, (b) weak positivity, (c) moderate positivity staining of cytoplasm, (d) moderate nuclear staining, (e) strong SOX13 expression in benign islet cells with negative acinar staining, and (f) strong SOX13 expression in benign islet cells with positive acinar staining.

Article Snippet: For target gene knockdown functional experiments, predesigned pool of 3 target-specific 19–25 nt siRNAs designed to knock down SOX13 gene expression (Santa Cruz Biotech., sc-38424), a control (nontransfected), and a scrambled control siRNA (sc-37007) were used.

Techniques: Immunohistochemistry, Staining, Expressing

Journal: Journal of Oncology

Article Title: Genomic Profiling and Functional Analysis of let-7c miRNA-mRNA Interactions Identify SOX13 to Be Involved in Invasion and Progression of Pancreatic Cancer

doi: 10.1155/2020/2951921

Figure Lengend Snippet: (a) Confirmation of knockdown of SOX13 by siRNA by qRT-PCR. SiRNA inhibition of SOX13 (siSOX13) significantly reduced (b) invasion and (c) colony formation efficiency in Panc-1 cell line ( n = 3).

Article Snippet: For target gene knockdown functional experiments, predesigned pool of 3 target-specific 19–25 nt siRNAs designed to knock down SOX13 gene expression (Santa Cruz Biotech., sc-38424), a control (nontransfected), and a scrambled control siRNA (sc-37007) were used.

Techniques: Knockdown, Quantitative RT-PCR, Inhibition

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: The expression of SOX13 in BC. (A) Human SOX13 expression levels were explored by TIMER database in 33 types of cancers (*P < 0.05, **P < 0.01, ***P < 0.001). (B) SOX13 expression profiles of normal and tumor tissues by Kaplan–Meier Plotter. (C) The protein expression of SOX13 was detected to be overexpressed in BC tissues versus normal samples.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: The expression of SOX13 in BC (IHC). (A) Tumor (B) Normal (upper: bar = 500μm, lower: bar = 50μm).

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: Effect of SOX13 on gene mutations in BC. (A) alteration frequency of SOX13 in each cancer of TCGA. (B) Correlation between CAN and SOX13 expression. (C) Correlation between methylation and SOX13 mRNA expression. (D) Top 10 mutated genes in SOX13 high and low expression group. (E) Significant different mutation genes in SOX13 low and high expression groups.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing, Methylation, Mutagenesis

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: Association between SOX13 expression and clinicopathologic features.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: Spearman analysis of correlation between SOX13 and clinicopathological.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: The higher the SOX13 expression, the worse the OS. (A) Kaplan-Meier OS curves of BC patients according to the expression of SOX13. (B) GEPIA. (C) UALCAN. (D) Kaplan-Meier plotter.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: Univariate and multivariate Cox proportional hazards analysis of SOX13 expression and OS for BC patients.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: SOX13 co-expression genes in BC (LinkedOmics) and enrichment analysis. (A) Genes whose expression was highly associated with SOX13 confirmed by Pearson test in BC cohort. Heatmaps showing the top 50 genes negatively (B) and positively (C) correlated with SOX13 in BC.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: The GO and KEGG enrichment analysis of SOX13 co-expressed genes.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques:

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: The role of SOX13 in tumor microenvironment. (A) The role of SOX13 on immune infiltration using the data from the TIMER2 database. (B) The role of SOX13 on immune cell infiltration using data from ImmuCellAI database. (C) The role of SOX13 on immune cell infiltration in the setting of breast cancer. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques:

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: SOX13 correlation with immunomodulatory genes. (A) Immunosuppressive genes. (B) Chemokine receptor genes. (C) Chemokine genes. (D) Wnt/β-catenin signaling genes. (E) TGF-β1 signaling genes. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques:

Journal: Frontiers in Immunology

Article Title: SOX13 is a novel prognostic biomarker and associates with immune infiltration in breast cancer

doi: 10.3389/fimmu.2024.1369892

Figure Lengend Snippet: | Drug sensitivity analysis. (A-C) The top 3 SOX13 positively correlated drugs from the GDSC2 database. (D, F) The top 3 SOX13 negatively correlated drugs from the GDSC2 database. (G-L) Differential expression of IC50 between different drugs in high and low SOX13 expression groups.

Article Snippet: The anti-SOX13 antibody (TA321719S, ORIGENE, USA) was incubated with the samples for a whole night at 4°C.

Techniques: Expressing

Journal: Cancers

Article Title: DNA Methylation Clusters and Their Relation to Cytogenetic Features in Pediatric AML

doi: 10.3390/cancers12103024

Figure Lengend Snippet: Top 50 methylation probes identified by supervised analysis of DNA methylation with to 50 unique methylation signatures by individual cytogenetic risk feature shown.

Article Snippet: cg04596071 , 7 , MAD1L1 , 4.51 × 10 −14 , cg05716567 , 8 , ZC3H3 , 3.91 × 10 −25 , cg09107053 , 1 , C1orf198 , 1.66 × 10 −11 , cg01826444 , 1 , FNDC7 , 2.40 × 10 −6 , cg14876117 , 14 , PYGL , 2.62 × 10 −9 , cg14663914 , 19 , AZU1 , 3.20 × 10 −8.

Techniques: Methylation, DNA Methylation Assay

Journal: Bioengineered

Article Title: Circular RNA SOX13 promotes malignant behavior and cisplatin resistance in non-small cell lung cancer through targeting microRNA-3194-3p/microtubule-associated protein RP/EB family member 1

doi: 10.1080/21655979.2021.1997223

Figure Lengend Snippet: CircSOX13 promotes the malignant behavior of NSCLC via miR-3194-3p/MAPRE1 axis . After transfecting oe-SOX13 and si-MAPRE1, A. RT-qPCR or western blot to detect circSOX13, miR-3194-3p and MAPRI1 expression; B. CCK-8 to detect A549 and H1299 viability; C. Edu analysis to detect A549 and H1299 proliferation; D. Flow cytometry to detect A549 and H1299 apoptosis rate; E. Transwell to detect A549 and H1299 invasion and migration abilities; the values were expressed as mean ± SD (n = 3); versus the oe-NC group, * P < 0.05; versus the oe-SOX13 + si-NC group, ^ P < 0.05.

Article Snippet: Short harpin RNA targeting circRNA SOX13 (sh-SOX13), short hairpin RNA NC (sh-NC), small interfering RNA targeting MAPRE1 (si-MAPRE1), small interfering RNA NC (si-NC), miR-3194-3p mimic/inhibitor and mimic/inhibitor NC were purchased from Sangon Biotech (Shanghai, China).

Techniques: Quantitative RT-PCR, Western Blot, Expressing, CCK-8 Assay, Flow Cytometry, Migration

Journal: Bioengineered

Article Title: Circular RNA SOX13 promotes malignant behavior and cisplatin resistance in non-small cell lung cancer through targeting microRNA-3194-3p/microtubule-associated protein RP/EB family member 1

doi: 10.1080/21655979.2021.1997223

Figure Lengend Snippet: CircSOX13 promotes cisplatin resistance in NSCLC via miR-3194-3p /MAPRE1 axis . A. The expression of MAPRE1 and miR-3194-3p in A549/DDP and H1299/DDP cells after co-transfection oe-SOX13 and miR-3194-3p mimic detected by RT-qPCR or Western blot; B. IC 50 values of A549/DDP and H1299/DDP cells after co-transfection oe-circSOX13 and miR-3194-3p mimic detected by CCK-8; C. DNA replication in A549/DDP and H1299/DDP cells after co-transfection with oe-circSOX13 and miR-3194-3p mimic detected by Edu; D. Apoptosis of A549/DDP and H1299/DDP cells after co-transfection with oe-circSOX13 and miR-3194-3p mimic detected by flow cytometry; E. Transwell to detect the invasion and migration abilities of A549/DDP and H1299/DDP cells after co-transfection with oe-circSOX13 and miR-3194-3p mimic. The values were expressed as mean ± SD (n = 3); versus the oe-NC group, * P < 0.05; versus the oe-SOX13 + mimic NC group, ^ P < 0.05.

Article Snippet: Short harpin RNA targeting circRNA SOX13 (sh-SOX13), short hairpin RNA NC (sh-NC), small interfering RNA targeting MAPRE1 (si-MAPRE1), small interfering RNA NC (si-NC), miR-3194-3p mimic/inhibitor and mimic/inhibitor NC were purchased from Sangon Biotech (Shanghai, China).

Techniques: Expressing, Cotransfection, Quantitative RT-PCR, Western Blot, CCK-8 Assay, Flow Cytometry, Migration