ddx39  (Proteintech)

Journal: iScience

Article Title: PABPC1 mediates degradation of C9orf72 -FTLD/ALS GGGGCC repeat RNA

doi: 10.1016/j.isci.2024.109303

Figure Lengend Snippet:

Article Snippet: Mouse anti-BAT1/DDX39 (WB: 1:200) , Santa Cruz Biotechnology , Cat# sc-271395; RRID: AB_10609494.

Techniques: FLAG-tag, Virus, Recombinant, Magnetic Beads, Plasmid Preparation, Protease Inhibitor, Blocking Assay, Reverse Transcription, Silver Staining, In Situ, Expressing, Construct, Software, Molecular Weight, Laser-Scanning Microscopy, Real-time Polymerase Chain Reaction

Journal: Cell reports

Article Title: Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export

doi: 10.1016/j.celrep.2022.111106

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse anti-UAP56 (BAT1) monoclonal (IF 1:50) , Santa Cruz Biotechnology , Cat# sc-271395; RRID:AB_10609494.

Techniques: Virus, Recombinant, Extraction, TaqMan Assay, CRISPR, Expressing, Construct, Software, Translocation Assay, Microscopy, Real-time Polymerase Chain Reaction

Journal: Cell reports

Article Title: Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export

doi: 10.1016/j.celrep.2022.111106

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse anti-UAP56 (BAT1) monoclonal (IF 1:50) , Santa Cruz Biotechnology , Cat# sc-271395; RRID:AB_10609494.

Techniques: Virus, Recombinant, Extraction, TaqMan Assay, CRISPR, Expressing, Construct, Software, Translocation Assay, Microscopy, Real-time Polymerase Chain Reaction

Journal: Cell reports

Article Title: Proteomics reveal cap-dependent translation inhibitors remodel the translation machinery and translatome

doi: 10.1016/j.celrep.2021.109806

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Primary antibodies: puromycin (Kerafast #Equation 0001, 1:1000); eIF4A1 (Abcam #31217, 1:1000); eIF4A2 (SCBT #sc-137148, 1:1000); CD98hc (CST #13180S, 1:500); GEF-H1 (Proteintech #24472-1-AP, 1:1000); SPEN (Novus Biologicals #NB100-58799); CEP170 (ThermoFisher Scientific #41-3200, 1:1000); DHX36 (Proteintech #13159-1-AP, 1:1000); DDX39 (Proteintech #11723-1-AP, 1:1000); JNK (CST #4672S, 1:1000); phospho-JNK (CST #4668S, 1:1000); c-JUN (CST #9165S, 1:1000); phospho-c-JUN (CST #9261S, 1:1000); RHOA (CST #2117S, 1:1000); RHO (ThermoFisher Scientific #16116, 1:1000); p130Cas (CST #13846S, 1:1000); phospho-p130Cas (CST #4011S, 1:1000); AKT (CST #4685S, 1:1000); phospho-AKT (CST #4060S, 1:1000); MCL-1 (CST #94296S, 1:1000); CPSF73 (Proteintech #11609-1-AP, 1:1000); eEF1ε1 (Proteintech #10805-1-AP, 1:1000); DDX17 (Proteintech #19910-1-AP); PABPN1 (Proteintech #66807-1-Ig); Histone H3 (CST #4499S, 1:2000); GAPDH (CST #5174T, 1:2000); CYPB (ThermoFisher Scientific #PA1-027A, 1:10000).

Techniques: Plasmid Preparation, Derivative Assay, Recombinant, Protease Inhibitor, cDNA Synthesis, SYBR Green Assay, Mass Spectrometry, Construct, Software

Journal: Cell reports

Article Title: Proteomics reveal cap-dependent translation inhibitors remodel the translation machinery and translatome

doi: 10.1016/j.celrep.2021.109806

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: DDX39 , Proteintech , Cat#11723-1-AP; RRID:AB_10858318.

Techniques: Plasmid Preparation, Derivative Assay, Recombinant, Protease Inhibitor, cDNA Synthesis, SYBR Green Assay, Mass Spectrometry, Construct, Software

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: Pan-cancer analysis of DDX39 expression. A. Expression levels of DDX39 in 20 different cancer types, derived from Oncomine database. B. Differential expression levels of DDX39 in 33 cancer types and corresponding normal tissues from TCGA database, * p <0.05, ** p <0.01, *** p <0.001, **** p <0.0001. C. Differential expression levels of DDX39 in paired cancer and adjacent normal tissues of 22 cancer types from TCGA database, * p <0.05, ** p <0.01, *** p <0.001, **** p <0.0001.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing, Derivative Assay, Quantitative Proteomics

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: DDX39 is highly expressed in renal clear cell carcinoma. A. DDX39 expression levels in GEO GSE40435 dataset, p <0.0001. B. DDX39 expression levels in GEO GSE16449 dataset, p <0.0001. C. RT-PCR results of DDX39 expressions of samples from Changzheng cohort, n=29, T: tumor, N: normal tissue, p <0.05. D. Representative IHC images of DDX39 expression retrieved from HPA database. E. Western blot analysis of DDX39 protein expression between the adjacent tissue (AT) and tumor (T) from Changzheng cohort. The gray value shows the difference between two groups, ** p <0.01, *** p <0.001.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Western Blot

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: DDX39 expression is related to clinical prognosis. A. DDX39 expression in TCGA ccRCC patients with different histological grade, * p <0.05, *** p <0.001, **** p <0.0001. B. DDX39 expression in TCGA ccRCC patients with different AJCC clinical stage, * p <0.05, ** p <0.01, *** p <0.001, **** p <0.0001. C. Kaplan-Meier analysis of OS of TCGA ccRCC patients with high or low DDX39 expression, p<0.0001. D. Kaplan-Meier analysis of PFI of TCGA ccRCC patients with high or low DDX39 expression, p<0.0001. E. Multivariate COX analysis on DDX39 expression and other clinical factor associated with OS in TCGA ccRCC patients, ** p <0.001. F. Time dependent ROC curve on DDX39 in TCGA ccRCC patients.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: Univariate and multivariate analysis of the correlation between DDX39 expression and overall survival in TCGA ccRCC patients

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: DDX39 expression is related to clinical prognosis in RCC patients of Changhai cohort. A. Representative immunohistochemical images of DDX39 expression in ccRCC and adjacent tissues, scale bar = 50um. B. Kaplan-Meier analysis of the disease-free survival of ccRCC patients with high or low DDX39 expression. C. Kaplan-Meier analysis of the overall survival of ccRCC patients with high or low DDX39 expression. D. Multivariate analyses of factors associated with overall survival in ccRCC patients, n = 186, * p <0.05. E. Multivariate analyses of factors associated with disease-free survival in ccRCC patients, n = 186, * p <0.05.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing, Immunohistochemical staining

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: Correlation between DDX39 and clinicopathological features in Changhai ccRCC cohort

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques:

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: Univariate and multivariate analysis for overall survival of ccRCC patients in Changhai cohort

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: DDX39 functions as RNA processing protein and associates with MYC and cell cycle acceleration hallmarks in GO and GSEA analysis. A. DDX39 is associated with RNA processing functions in BP module of GO analysis. B. DDX39 is associated with MYC_targets_V1 hallmark in GSEA analysis, p.adjust=0.009. C. DDX39 is associated with MYC_targets_V2 hallmark in GSEA analysis, p.adjust<0.001. D. DDX39 is associated with E2F hallmark in GSEA analysis, p.adjust<0.001. E. DDX39 is associated with G2M hallmark in GSEA analysis, p.adjust<0.001.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques:

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: DDX39 promotes renal cancer cell proliferation, migration and invasion in vitro. A. Cell proliferation of A498. Si-A498: negative control, si-DDX39: treated with si-RNA, bars indicated SD. *<0.05, **P<0.01. B. Cell colonies of A498 after treated with si-DDX39, **P<0.01. C. Cell migration of A498 after treated with si-DDX39, ***P<0.001, scale bar = 200um. D. Cell invasion of A498 after treated with si-DDX39, ****P<0.0001, scale bar = 200um. E. Cell proliferation of OS-RC-2. Control: EV, DDX39: treated with DDX39 overexpression plasmid, bars indicated SD. *P<0.05, **P<0.01, ***P<0.001. F. Cell colonies of OS-RC-2 after treated with DDX39 overexpression plasmid, **P<0.01. G. Cell migration of OS-RC-2 after treated with DDX39 overexpression plasmid, ***P<0.001, scale bar = 200um.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Migration, In Vitro, Negative Control, Control, Over Expression, Plasmid Preparation

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: Increased DDX39 is related to higher Estimatescores and immunotherapy predicting pathways in heatmap and ssGESA analysis. A. Heatmap of associations between Estimatescores and DDX39 in TCGA ccRCC patients. B. ssGSEA analysis of associations between immunotherapy predicting pathways and DDX39 in TCGA ccRCC patients.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques:

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: DDX39 expression is related to immune infiltration and associates with the antigen presentation process in ccRCC patients. A. DDX39 is associated with multiple immune cell infiltration in ccRCC in TIMER2.0 database. B. Different DDX39 expression in 28 immune cells in ccRCC patients from TCGA database, * p <0.05, ** p <0.01, *** p <0.001, **** p <0.0001. C. Associations between DDX39 expression and NES of 28 immune cells in ccRCC from TCGA database. D. DDX39 is related to a variety of immune processes in ccRCC from TCGA database in GO analysis.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing, Immunopeptidomics

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: Increased DDX39 expression associates with higher inhibitory immune genes (PD-1, CD38, LGALS9, FCRL4, LAG3, KLRD1, CD200 and TNFRSF4) in ccRCC patients.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: Increased DDX39 is related to higher immune dysfunction scores and worse immune check-point therapy efficacy in ccRCC patients. A. Pearson's correlation analysis between DDX39 and immune dysfunction score in TCGA ccRCC patients, n=531, r Pearson =0.38, p <0.0001. B. Pearson's correlation analysis between DDX39 and Tidescore in TCGA ccRCC patients, n=531, r Pearson =0.1, p =0.02. C. Immune checkpoint therapy response rates in TCGA ccRCC patients with high and low DDX39 expression in TIDE analysis, p =0.011.

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing

Journal: International Journal of Biological Sciences

Article Title: DDX39 as a predictor of clinical prognosis and immune checkpoint therapy efficacy in patients with clear cell renal cell carcinoma

doi: 10.7150/ijbs.62553

Figure Lengend Snippet: Univariate and multivariate analysis for disease-free survival of ccRCC patients in Changhai cohort

Article Snippet: Immunohistochemical (IHC) stanning was performed on Changhai ccRCC tissue microarray using DDX39 antibody (DDX39A Polyclonal Antibody, 11723-1-AP, Proteintech, diluted at 1:50).

Techniques: Expressing