Journal: Cell Reports Methods

Article Title: MPA PASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays

doi: 10.1016/j.crmeth.2021.100136

Figure Lengend Snippet: Detection antibodies used

Article Snippet: CA9 , Miltenyi Biotec , Cat# 130-110-058; RRID: AB_2651327.

Techniques: Labeling, Recombinant

Journal: Cell Reports Methods

Article Title: MPA PASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays

doi: 10.1016/j.crmeth.2021.100136

Figure Lengend Snippet:

Article Snippet: CA9 , Miltenyi Biotec , Cat# 130-110-058; RRID: AB_2651327.

Techniques: Clinical Proteomics, Recombinant, Saline, Modification, Software

Journal: Cell Death & Disease

Article Title: Sanguinarine inhibits epithelial–mesenchymal transition via targeting HIF-1α/TGF-β feed-forward loop in hepatocellular carcinoma

doi: 10.1038/s41419-019-2173-1

Figure Lengend Snippet: a MHCC-97H and SMMC-7721 cells were treated with 100 μM CoCl 2 or incubated in 1% O 2 for 24 h. HIF1A, CA9, VEGF, and TGFB1 mRNA expression values were assessed by RT-qPCR. Gene expression is normalized to ACTB. MHCC-97H and SMMC-7721 cells were treated with 100 μM CoCl 2 or incubated in 1% O 2 for 24 or 48 h. b TGF-β secretion was determined by ELISA. Mean + SEM ( n = 5), * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001, one-way ANOVA followed by Bonferroni posttest in comparison with control. c HIF-1α, ARNT, PHD2, CA9, and TGF-β (SN, supernatant) protein levels were determined by western blotting. Quantification plots are shown below. d MHCC-97H and SMMC-7721 cells were stimulate d with 10 ng/mL TGF-β for 24 h. HIF1A, CA9, and VEGF mRNA expression values were assessed by RT-qPCR. Gene expression is normalized to ACTB. e MHCC-97H and SMMC-7721 cells were stimulat e d with 0, 5, and 10 ng/mL TGF-β for 24 h. HIF-1α, ARNT, PHD2 and VEGF, and CA9 protein levels were examined by western blotting. Quantification plots are shown on the right. f MHCC-97H and SMMC-7721 cells were treated with 100 μM CoCl 2 in the presence of absence of 0.5 μM TGF-β receptor inhibitor LY2157299. HIF1A expression was assessed by RT-qPCR. Gene expression is normalized to ACTB and control group was assigned as 1. g MHCC-97H and SMMC-7721 cells were treated with 100 μM CoCl 2 in the presence of absence of 0.5 μM TGF-β receptor inhibitor LY2157299. HIF-1α and CA9 were determined by western blotting. Quantification plots are shown below. h MHCC-97H and SMMC-7721 cells were treated with 100 μM CoCl 2 in the presence of absence of 0.5 μM LY2157 2 99 for 48 h. LY2157299 was removed and treated with 5 ng/mL TGF-β for additional 24 h. HIF1A expression was assessed by RT-qPCR. Gene expression is normalized to ACTB and shown as fold change. Data were expressed as mean ± SEM ( n = 3). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001 compared with untreated control cells or as indicated. Data are representative of three independent experiments.

Article Snippet: E-cadherin, N-cadherin, Vimentin, Snail, VEGF, ARNT, CA9, PHD2, TGF-β rabbit mAb, Phospho-AKT, HIF-1α, GAPDH, and β-actin mouse mAb were obtained from Protein Technology Group (Chicago, Illinois, USA), and PI3K-p110α, PI3K-p110β, Phospho-p85, Phospho-Smad2/3, and α-SMA rabbit mAb were purchased from Cell Signaling (Boston, Massachusetts, USA).

Techniques: Incubation, Expressing, Quantitative RT-PCR, Gene Expression, Enzyme-linked Immunosorbent Assay, Comparison, Control, Western Blot

Journal: Cell Death & Disease

Article Title: Sanguinarine inhibits epithelial–mesenchymal transition via targeting HIF-1α/TGF-β feed-forward loop in hepatocellular carcinoma

doi: 10.1038/s41419-019-2173-1

Figure Lengend Snippet: a MHCC-97H cells were treated with sanguinarine in the absence or presence of 1% O 2 for 12 h. HIF-1α (red), ARNT (green), DAPI (blue) staining, and 3-channel merged images indicated the nuclear translocation of HIF-1α. Scale bars, 200 μm. MHCC-97H and SMMC-7721 cells were treated with different concentrations of sanguinarine in the absence or presence of 1% O 2 or 100 μM CoCl 2 for 24 h. b HIF-1α, CA9, VEGF, N-cadherin, and Vimentin expression levels were assessed by western blotting. Quantification plots are shown on the right. Data were expressed as mean ± SEM ( n = 3). The results shown were representative of three independent experiments. c VEGF and d TGF-β production was analyzed by ELISA. Data are represented as mean + SEM. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001, one-way ANOVA followed by Bonferroni posttest in comparison with control. # P < 0.05, ## P < 0.01, ### P < 0.001, #### P < 0.0001 one-way ANOVA followed by Bonferroni posttest in comparison with CoCl 2 or 1% O 2 samples.

Article Snippet: E-cadherin, N-cadherin, Vimentin, Snail, VEGF, ARNT, CA9, PHD2, TGF-β rabbit mAb, Phospho-AKT, HIF-1α, GAPDH, and β-actin mouse mAb were obtained from Protein Technology Group (Chicago, Illinois, USA), and PI3K-p110α, PI3K-p110β, Phospho-p85, Phospho-Smad2/3, and α-SMA rabbit mAb were purchased from Cell Signaling (Boston, Massachusetts, USA).

Techniques: Staining, Translocation Assay, Expressing, Western Blot, Enzyme-linked Immunosorbent Assay, Comparison, Control

Journal: Cell Death & Disease

Article Title: Sanguinarine inhibits epithelial–mesenchymal transition via targeting HIF-1α/TGF-β feed-forward loop in hepatocellular carcinoma

doi: 10.1038/s41419-019-2173-1

Figure Lengend Snippet: a HepG2 cells were treated with different concentrations of sanguinarine in the absence or presence of 10 ng/mL TGF-β for 24 h. Snail (green), α-SMA (green), p-Smad2/3 (green), DAPI (blue) staining and 2-channel merged images indicated the nuclear translocation of Snail and p-Smad2/3, and expression of α-SMA. The results shown were representative of three independent experiments. Scale bars, 200 μm. b SMMC-7721 cells were treated with different concentrations of sanguinarine in the absence or presence of 10 ng/mL TGF-β. Protein levels of N-cadherin, Vimentin, and Snail were analyzed by western blotting. Quantification plots are shown below. c MHCC-97H cells were treated with different concentrations of sanguinarine in the absence or presence of 10 ng/mL TGF-β. Protein levels of N-cadherin, Snail, HIF-1α, ARNT, PHD2, and CA9 were analyzed by western blotting. GAPDH or β-actin served as controls. Quantification plots are shown below. Western blot analysis of p100α, p110β, p-p85, and p-AKT expression were demonstrated in d HepG2 and e SMMC-7721 cells treated with indicated concentrations of sanguinarine in the absence or presence of 10 ng/mL TGF-β for 48 h. Quantification plots are shown below. Data were expressed as mean ± SEM ( n = 3). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001 compared with untreated control cells. The results shown were representative of three independent experiments. # P < 0.05, ## P < 0.01, ### P < 0.001, #### P < 0.0001 one-way ANOVA followed by Bonferroni posttest in comparison with TGF-β-treated samples.

Article Snippet: E-cadherin, N-cadherin, Vimentin, Snail, VEGF, ARNT, CA9, PHD2, TGF-β rabbit mAb, Phospho-AKT, HIF-1α, GAPDH, and β-actin mouse mAb were obtained from Protein Technology Group (Chicago, Illinois, USA), and PI3K-p110α, PI3K-p110β, Phospho-p85, Phospho-Smad2/3, and α-SMA rabbit mAb were purchased from Cell Signaling (Boston, Massachusetts, USA).

Techniques: Staining, Translocation Assay, Expressing, Western Blot, Control, Comparison

Journal: bioRxiv

Article Title: Chromosome-Specific Aneuploidy Engineering via dCas9-Induced Centromeric Chromatin Relaxation

doi: 10.1101/2025.04.25.650684

Figure Lengend Snippet: a , Schematics showing the experiment setup of Chr3 aneuploidy engineering using CRISPRt with Chr3-sg2 (Chr3-Ct) or NT-sg1 (CTRL), and VHL allele-specific KO ( VHL -ASK) in K1088N PTECs. Cells were cultured for 7 days (D7) or 11 days (D7+4) after treatments. Cells with Chr3-Ct or VHL -ASK on D7+4 were selected for CA9-positive (CA9+) cells with flow sorting. The six samples fixed for scRNA-seq are marked in red. b, Heatmaps showing single-cell chromosome copy number profiles inferred from scRNA-seq data of the indicated samples. The number of cells analysed (n) is shown. Rows represent individual cells and columns represent chromosomes. Copy number status is shown in blue (loss), red (gain) or white (neutral). c, Violin plots showing InferCNV residual expression for Chr3p and Chr3q of the indicated samples. The dots represent individual cells. The blue and red dashed lines represent the thresholds (see Methods) for copy number loss and gain, respectively. The cell proportions with the indicated copy number status are shown in the tables.

Article Snippet: Cells were stained with 1:50 diluted anti-CA9-PE antibody (Miltenyi, 130-131-321) in flow sorting buffer (1% bovine serum albumin (BSA) and 1μM EDTA in PBS) for 30 min at 4 °C in the dark.

Techniques: Cell Culture, Expressing

Journal: bioRxiv

Article Title: Chromosome-Specific Aneuploidy Engineering via dCas9-Induced Centromeric Chromatin Relaxation

doi: 10.1101/2025.04.25.650684

Figure Lengend Snippet: a , Schematics showing the expected genotypes generated after Chr3-Ct or VHL -ASK in K1088N PTECs with the corresponding VHL status annotated ( VHL + for VHL proficient, and VHL- for VHL loss) and the target genotypes with VHL loss enriched by CA9-positive (CA9+) flow sorting. b, Scatter plots showing the CA9 and DAPI staining intensities of K1088N PTECs after the indicated treatment. The rectangular box shows the gating strategy to flow sort for live (DAPI-) CA9-positive (CA9+) cells. c, Violin plots showing the signature scores of a curated HIF pathway activation gene set (see Methods) in K1088N PTECs after the indicated treatment. The dots represent individual cells. The dashed line represents the calculated threshold (see Methods) for defining cells with a high (HIF-High) or a low (HIF-Low) HIF pathway signature score, used for assigning VHL proficient ( VHL +) or VHL loss ( VHL- ) status.

Article Snippet: Cells were stained with 1:50 diluted anti-CA9-PE antibody (Miltenyi, 130-131-321) in flow sorting buffer (1% bovine serum albumin (BSA) and 1μM EDTA in PBS) for 30 min at 4 °C in the dark.

Techniques: Generated, Staining, Activation Assay