jhc7 cells  (ATCC)


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    ATCC jhc7 cells
    Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines <t>JHC7</t> and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.
    Jhc7 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities"

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    Journal: Frontiers in Oncology

    doi: 10.3389/fonc.2022.941046

    Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.
    Figure Legend Snippet: Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.

    Techniques Used: Transfection, Western Blot, Negative Control

    Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.
    Figure Legend Snippet: Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.

    Techniques Used: CCK-8 Assay, Proliferation Assay

    jhc7 cells  (ATCC)


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    ATCC jhc7 cells
    Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines <t>JHC7</t> and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.
    Jhc7 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities"

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    Journal: Frontiers in Oncology

    doi: 10.3389/fonc.2022.941046

    Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.
    Figure Legend Snippet: Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.

    Techniques Used: Transfection, Western Blot, Negative Control

    Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.
    Figure Legend Snippet: Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.

    Techniques Used: CCK-8 Assay, Proliferation Assay

    human chordoma cell lines jhc7  (ATCC)


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    ATCC human chordoma cell lines jhc7
    Summary of clinical information of <t> chordoma </t> tumor samples and classification.
    Human Chordoma Cell Lines Jhc7, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities"

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    Journal: Frontiers in Oncology

    doi: 10.3389/fonc.2022.941046

    Summary of clinical information of  chordoma  tumor samples and classification.
    Figure Legend Snippet: Summary of clinical information of chordoma tumor samples and classification.

    Techniques Used:

    Characterization of the proteome and phosphoproteome in chordoma tumor and normal tissues. (A) General pipeline of (phospho)peptide enrichment and the quantitative mass spectrometric protocol followed by pathway analyses and biochemical validation. (B, C) Principal component analysis (PCA) of the quantified proteome (B) and quantified phosphoproteome (C) . (D, E) Statistical analysis of the 4D label-free proteomic (D) and phosphoproteomic (E) datasets.
    Figure Legend Snippet: Characterization of the proteome and phosphoproteome in chordoma tumor and normal tissues. (A) General pipeline of (phospho)peptide enrichment and the quantitative mass spectrometric protocol followed by pathway analyses and biochemical validation. (B, C) Principal component analysis (PCA) of the quantified proteome (B) and quantified phosphoproteome (C) . (D, E) Statistical analysis of the 4D label-free proteomic (D) and phosphoproteomic (E) datasets.

    Techniques Used:

    Targeted proteomic study and altered expression of Wnt-signaling-related proteins. (A) Statistical comparison of regulated proteins between chordoma tissues (CT) and their paired normal adjacent muscle tissues (CN) by Q category. Q1, 0 < ratio ≤ 0.5, corresponding to downregulated proteins; Q2, 0.5 < ratio ≤ 0.667; Q3, 1.5 < ratio ≤ 2; Q4, ratio >2, corresponding to upregulated proteins. Protein numbers for Q1-Q4 are 364/35/171/775, respectively. (B) Volcano plot of the distributional patterns of statistical significance (-log P value) and magnitude of the changes (log 2 FC) for all DEPs. (C) Unsupervised hierarchical clustering heatmap of the significantly regulated proteins identified from chordoma tissues. Unique proteins (n=1,139; rows) were significantly identified from nine paired samples (columns). TP, tumor proteins; NP, normal proteins. Unsupervised hierarchical clustering was performed using the Cluster program with Pearson correlation and pairwise complete-linkage analyses. (D) KEGG pathway-enrichment analysis was executed to identify important pathways that depended upon all DEPs. The colored blocks that correspond to functional classification indicate the magnitude of enrichment, and are displayed by colors ranging from blue (weak enrichment) to red (strong enrichment). (E–N) Relative normalized expression of CTNNB1 (E) , RUVBL1 (F) , RAC1 (G) , RAC2 (H) , RHOA (I) , ROCK2 (J) , PRKACA (K) , CAMK2G (L) , CAMK2D (M) , and CAMK2B (N) . The vertical axis signifies log (2). CN, blue; CT, red. Student’s paired t-test was applied to distinguish the expression differences; *, p < 0.05, **, p < 0.01, ***, p < 0.001.
    Figure Legend Snippet: Targeted proteomic study and altered expression of Wnt-signaling-related proteins. (A) Statistical comparison of regulated proteins between chordoma tissues (CT) and their paired normal adjacent muscle tissues (CN) by Q category. Q1, 0 < ratio ≤ 0.5, corresponding to downregulated proteins; Q2, 0.5 < ratio ≤ 0.667; Q3, 1.5 < ratio ≤ 2; Q4, ratio >2, corresponding to upregulated proteins. Protein numbers for Q1-Q4 are 364/35/171/775, respectively. (B) Volcano plot of the distributional patterns of statistical significance (-log P value) and magnitude of the changes (log 2 FC) for all DEPs. (C) Unsupervised hierarchical clustering heatmap of the significantly regulated proteins identified from chordoma tissues. Unique proteins (n=1,139; rows) were significantly identified from nine paired samples (columns). TP, tumor proteins; NP, normal proteins. Unsupervised hierarchical clustering was performed using the Cluster program with Pearson correlation and pairwise complete-linkage analyses. (D) KEGG pathway-enrichment analysis was executed to identify important pathways that depended upon all DEPs. The colored blocks that correspond to functional classification indicate the magnitude of enrichment, and are displayed by colors ranging from blue (weak enrichment) to red (strong enrichment). (E–N) Relative normalized expression of CTNNB1 (E) , RUVBL1 (F) , RAC1 (G) , RAC2 (H) , RHOA (I) , ROCK2 (J) , PRKACA (K) , CAMK2G (L) , CAMK2D (M) , and CAMK2B (N) . The vertical axis signifies log (2). CN, blue; CT, red. Student’s paired t-test was applied to distinguish the expression differences; *, p < 0.05, **, p < 0.01, ***, p < 0.001.

    Techniques Used: Expressing, Functional Assay

    KiPNA analysis and the expression validation of specific proteins. (A) Kinase-pathway network analysis (KiPNA) indicating the proteomic and phosphoproteomic signaling network in chordoma. (B) Fourteen and 29 kinases were conjectured to be negatively and positively regulated, respectively. (C) The elevated expression of brachyury-T, AURA, MOK, and CDK9 were verified by western immunoblotting analysis. The samples were derived from six independent patients who were distinct from the patients whose samples were used for mass spectrometry. T, tumor tissues; N, normal tissues. (D) Densitometric quantification of western blot results from (B) and presented relative to β-actin expression. The data represent the mean ± SD of each experiment carried out in triplicate.
    Figure Legend Snippet: KiPNA analysis and the expression validation of specific proteins. (A) Kinase-pathway network analysis (KiPNA) indicating the proteomic and phosphoproteomic signaling network in chordoma. (B) Fourteen and 29 kinases were conjectured to be negatively and positively regulated, respectively. (C) The elevated expression of brachyury-T, AURA, MOK, and CDK9 were verified by western immunoblotting analysis. The samples were derived from six independent patients who were distinct from the patients whose samples were used for mass spectrometry. T, tumor tissues; N, normal tissues. (D) Densitometric quantification of western blot results from (B) and presented relative to β-actin expression. The data represent the mean ± SD of each experiment carried out in triplicate.

    Techniques Used: Expressing, Western Blot, Derivative Assay, Mass Spectrometry

    Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.
    Figure Legend Snippet: Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.

    Techniques Used: Transfection, Western Blot, Negative Control

    Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.
    Figure Legend Snippet: Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.

    Techniques Used: CCK-8 Assay, Proliferation Assay

    Important proteins and pathways related to chordoma tumor size. (A) Unsupervised hierarchal clustering disclosed differential protein regulation between large and small chordomas. C1/C3/C4/C13 patients belonged to the large (L) group and C2/C5/CC8/C9/C12 to the small (S) group. (B) Combined KEGG pathway-enrichment analyses for both DEPs and DPPs are depicted as bubble charts. (C) Venn diagram of the proteomics and phosphoproteomics analyses for comparisons between L and S. (D) Seven proteins whose phosphorylation levels were augmented in both CT/CN and L/S groups.
    Figure Legend Snippet: Important proteins and pathways related to chordoma tumor size. (A) Unsupervised hierarchal clustering disclosed differential protein regulation between large and small chordomas. C1/C3/C4/C13 patients belonged to the large (L) group and C2/C5/CC8/C9/C12 to the small (S) group. (B) Combined KEGG pathway-enrichment analyses for both DEPs and DPPs are depicted as bubble charts. (C) Venn diagram of the proteomics and phosphoproteomics analyses for comparisons between L and S. (D) Seven proteins whose phosphorylation levels were augmented in both CT/CN and L/S groups.

    Techniques Used:

    jhc7 cells  (ATCC)


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    ATCC jhc7 cells
    XIST was upregulated in chordoma tissues. (A) The expression of XIST was examined by RT-qPCR in chordoma tissues and normal tissues. (B) The overall survival rate was analyzed by Kaplan-Meier analysis in chordoma patients with high and low XIST expression. (C and D) The localization of XIST was determined using RT-qPCR in the nuclear and cytosolic fractions of U-CH1 and <t>JHC7</t> cells. *** P < 0.001.
    Jhc7 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "XIST sponges miR-320d to promote chordoma progression by regulating ARF6"

    Article Title: XIST sponges miR-320d to promote chordoma progression by regulating ARF6

    Journal: Journal of Bone Oncology

    doi: 10.1016/j.jbo.2022.100447

    XIST was upregulated in chordoma tissues. (A) The expression of XIST was examined by RT-qPCR in chordoma tissues and normal tissues. (B) The overall survival rate was analyzed by Kaplan-Meier analysis in chordoma patients with high and low XIST expression. (C and D) The localization of XIST was determined using RT-qPCR in the nuclear and cytosolic fractions of U-CH1 and JHC7 cells. *** P < 0.001.
    Figure Legend Snippet: XIST was upregulated in chordoma tissues. (A) The expression of XIST was examined by RT-qPCR in chordoma tissues and normal tissues. (B) The overall survival rate was analyzed by Kaplan-Meier analysis in chordoma patients with high and low XIST expression. (C and D) The localization of XIST was determined using RT-qPCR in the nuclear and cytosolic fractions of U-CH1 and JHC7 cells. *** P < 0.001.

    Techniques Used: Expressing, Quantitative RT-PCR

    XIST knockdown inhibited the progression of chordoma cells. U-CH1 and JHC7 cells were transfected with sh-NC or sh-XIST. (A) The expression of XIST was measured by RT-qPCR. (B and C) MTT assay was used to assess cell viability. (D) DNA synthesis was assessed using EdU assay. (E) Colony formation assay was performed to detect the number of colonies. (F and G) Transwell assay was applied to assess cell migration and invasion. (H and I) Seahorse Bioscience XF96 extracellular flux analyzer was utilized to measure ECAR. (J) Lactate production was assessed using Lactate Assay kit. (K) Western blot assay was performed to analyze the protein levels of E-cad, N -cad, GLUT1, and LDHA. ** P < 0.01, *** P < 0.001.
    Figure Legend Snippet: XIST knockdown inhibited the progression of chordoma cells. U-CH1 and JHC7 cells were transfected with sh-NC or sh-XIST. (A) The expression of XIST was measured by RT-qPCR. (B and C) MTT assay was used to assess cell viability. (D) DNA synthesis was assessed using EdU assay. (E) Colony formation assay was performed to detect the number of colonies. (F and G) Transwell assay was applied to assess cell migration and invasion. (H and I) Seahorse Bioscience XF96 extracellular flux analyzer was utilized to measure ECAR. (J) Lactate production was assessed using Lactate Assay kit. (K) Western blot assay was performed to analyze the protein levels of E-cad, N -cad, GLUT1, and LDHA. ** P < 0.01, *** P < 0.001.

    Techniques Used: Transfection, Expressing, Quantitative RT-PCR, MTT Assay, DNA Synthesis, EdU Assay, Colony Assay, Transwell Assay, Migration, Lactate Assay, Western Blot

    XIST directly interacted with miR-320d. (A) Predicted binding sites between miR-320d and XIST were shown. (B) The expression of miR-320d was detected by RT-qPCR in U-CH1 and JHC7 cells transfected with miR-NC or miR-320d. (C and D) Dual-luciferase reporter assay was performed to examine the luciferase activity in U-CH1 and JHC7 cells co-transfected with miR-NC or miR-320d and XIST-WT or XIST-MUT. (E) The level of XIST was examined by RNA pull-down assay in U-CH1 and JHC7 cells transfected with Bio-miR-NC or Bio-miR-320d. (F) The expression of miR-320d was detected by RT-qPCR in chordoma tissues and normal tissues. (G) The correlation between XIST and miR-320d in chordoma tissues was analyzed. (H) The level of miR-320d was assessed by RT-qPCR in U-CH1 and JHC7 cells transfected with sh-NC or sh-XIST. *** P < 0.001.
    Figure Legend Snippet: XIST directly interacted with miR-320d. (A) Predicted binding sites between miR-320d and XIST were shown. (B) The expression of miR-320d was detected by RT-qPCR in U-CH1 and JHC7 cells transfected with miR-NC or miR-320d. (C and D) Dual-luciferase reporter assay was performed to examine the luciferase activity in U-CH1 and JHC7 cells co-transfected with miR-NC or miR-320d and XIST-WT or XIST-MUT. (E) The level of XIST was examined by RNA pull-down assay in U-CH1 and JHC7 cells transfected with Bio-miR-NC or Bio-miR-320d. (F) The expression of miR-320d was detected by RT-qPCR in chordoma tissues and normal tissues. (G) The correlation between XIST and miR-320d in chordoma tissues was analyzed. (H) The level of miR-320d was assessed by RT-qPCR in U-CH1 and JHC7 cells transfected with sh-NC or sh-XIST. *** P < 0.001.

    Techniques Used: Binding Assay, Expressing, Quantitative RT-PCR, Transfection, Luciferase, Reporter Assay, Activity Assay, Pull Down Assay

    MiR-320d exerted an anti-tumor role in chordoma cells. U-CH1 and JHC7 cells were transfected with miR-NC or miR-320d. (A-D) Cell proliferation was assessed by MTT assay, EdU assay and colony formation assay. (E and F) Cell migration and invasion were examined using transwell assay. (G and H) ECAR was detected using a Seahorse Bioscience XF96 extracellular flux analyzer. (I) Lactate production was evaluated by Lactate Assay kit. (J) The protein levels of E-cad, N -cad, GLUT1, and LDHA were determine by western blot assay. ** P < 0.01, *** P < 0.001.
    Figure Legend Snippet: MiR-320d exerted an anti-tumor role in chordoma cells. U-CH1 and JHC7 cells were transfected with miR-NC or miR-320d. (A-D) Cell proliferation was assessed by MTT assay, EdU assay and colony formation assay. (E and F) Cell migration and invasion were examined using transwell assay. (G and H) ECAR was detected using a Seahorse Bioscience XF96 extracellular flux analyzer. (I) Lactate production was evaluated by Lactate Assay kit. (J) The protein levels of E-cad, N -cad, GLUT1, and LDHA were determine by western blot assay. ** P < 0.01, *** P < 0.001.

    Techniques Used: Transfection, MTT Assay, EdU Assay, Colony Assay, Migration, Transwell Assay, Lactate Assay, Western Blot

    ARF6 was directly targeted by miR-320d. (A) The putative binding sites between miR-320d and ARF6 3′UTR were predicted by starBase. (B and C) The interaction between miR-320d and ARF6 was confirmed using dual-luciferase reporter assay in U-CH1 and JHC7 cells. (D) The expression of ARF6 mRNA was detect using RT-qPCR in chordoma tissues and normal tissues. (E and F) The correlation between ARF6 mRNA expression and miR-320d or XIST expression in chordoma tissues was analyzed. (G) The expression of ARF6 protein was examined by western blot assay in chordoma tissues and normal tissues. (H) The expression of miR-320d was tested using RT-qPCR in U-CH1 and JHC7 cells transfected with in-miR-NC or in-miR-320d. (I) ARF6 protein expression was measured by western blot assay in U-CH1 and JHC7 cells transfected with sh-NC, sh-XIST, sh-XIST + in-miR-NC, or sh-XIST + in-miR-320d. ** P < 0.01, *** P < 0.001.
    Figure Legend Snippet: ARF6 was directly targeted by miR-320d. (A) The putative binding sites between miR-320d and ARF6 3′UTR were predicted by starBase. (B and C) The interaction between miR-320d and ARF6 was confirmed using dual-luciferase reporter assay in U-CH1 and JHC7 cells. (D) The expression of ARF6 mRNA was detect using RT-qPCR in chordoma tissues and normal tissues. (E and F) The correlation between ARF6 mRNA expression and miR-320d or XIST expression in chordoma tissues was analyzed. (G) The expression of ARF6 protein was examined by western blot assay in chordoma tissues and normal tissues. (H) The expression of miR-320d was tested using RT-qPCR in U-CH1 and JHC7 cells transfected with in-miR-NC or in-miR-320d. (I) ARF6 protein expression was measured by western blot assay in U-CH1 and JHC7 cells transfected with sh-NC, sh-XIST, sh-XIST + in-miR-NC, or sh-XIST + in-miR-320d. ** P < 0.01, *** P < 0.001.

    Techniques Used: Binding Assay, Luciferase, Reporter Assay, Expressing, Quantitative RT-PCR, Western Blot, Transfection

    Knockdown of XIST suppressed chordoma cell proliferation, metastasis and glycolysis via reducing ARF6 expression. (A) ARF6 protein expression was determined by western blot assay in U-CH1 and JHC7 cells transfected with pcDNA or ARF6. (B-L) U-CH1 and JHC7 cells were transfected with sh-NC + pcDNA, sh-XIST + pcDNA or sh-XIST + ARF6. (B-E) MTT assay, EdU assay and colony formation assay were used to measure cell proliferation. (F and G) Cell migration and invasion were measured using transwell assay. (H and I) ECAR was examined by Seahorse Bioscience XF96 extracellular flux analyzer. (J) Lactate Assay kit was used to measure lactate production. (K and L) E-cad, N -cad, GLUT1, and LDHA protein expression were detected using western blot assay. ** P < 0.01, *** P < 0.001.
    Figure Legend Snippet: Knockdown of XIST suppressed chordoma cell proliferation, metastasis and glycolysis via reducing ARF6 expression. (A) ARF6 protein expression was determined by western blot assay in U-CH1 and JHC7 cells transfected with pcDNA or ARF6. (B-L) U-CH1 and JHC7 cells were transfected with sh-NC + pcDNA, sh-XIST + pcDNA or sh-XIST + ARF6. (B-E) MTT assay, EdU assay and colony formation assay were used to measure cell proliferation. (F and G) Cell migration and invasion were measured using transwell assay. (H and I) ECAR was examined by Seahorse Bioscience XF96 extracellular flux analyzer. (J) Lactate Assay kit was used to measure lactate production. (K and L) E-cad, N -cad, GLUT1, and LDHA protein expression were detected using western blot assay. ** P < 0.01, *** P < 0.001.

    Techniques Used: Expressing, Western Blot, Transfection, MTT Assay, EdU Assay, Colony Assay, Migration, Transwell Assay, Lactate Assay

    jhc7  (ATCC)


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    ATCC jhc7
    RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and <t>JHC7)</t> by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.
    Jhc7, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation"

    Article Title: RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation

    Journal: American Journal of Cancer Research

    doi:

    RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and JHC7) by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.
    Figure Legend Snippet: RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and JHC7) by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.

    Techniques Used: Expressing, Quantitative RT-PCR, Fluorescence, In Situ Hybridization, MTT Assay, Transwell Assay, Migration

    FUT4 was high expressed in chordoma tissues, and RP11-867G2.8 promoted the transcription of FUT4. (A) Western blot showing the protein expression of FUT4 in chordoma tissues and normal nucleus pulposus tissues. (B) Western blot showing the protein expression of FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. Expression of FUT4 mRNA in (C) U-CH1 and (D) JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.
    Figure Legend Snippet: FUT4 was high expressed in chordoma tissues, and RP11-867G2.8 promoted the transcription of FUT4. (A) Western blot showing the protein expression of FUT4 in chordoma tissues and normal nucleus pulposus tissues. (B) Western blot showing the protein expression of FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. Expression of FUT4 mRNA in (C) U-CH1 and (D) JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.

    Techniques Used: Western Blot, Expressing, Transfection, Negative Control, shRNA, Sequencing

    RP11-867G2.8 increased FUT4 mRNA stability and promoted FUT4 translation. qPCR validation of FUT4 enrichment versus input after RP11 RNA pull down using different specific probes as compared to a non-specific one in (A) U-CH1 and (B) JHC7 cells. The stability of FUT4 in transfected (C) U-CH1 and (D) JHC7 cells was measured by RT-qPCR in the presence of the transcription inhibitor Actinomycin D at the indicated time points. The half-life of FUT4 mRNA (t1/2) was calculated from each experiment shown in the graph. 18S rRNA was conducted as an internal control. (E, F) Sucrose density gradient fractionation and isolation of 40S/60S/80S and polysome cytoplasmic components for analysis, and (G, H) then polysome-fractionated samples analyzed by PCR. (I, J) Relative levels of FUT4 mRNAs in each ribosome fraction were quantified and normalized to RCN2 mRNA and plotted as a percentage of the total. Line 1-6, 40S/60S/80S; Line 7-12, polysome. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Data are from three independent polysome-profiling experiments. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.
    Figure Legend Snippet: RP11-867G2.8 increased FUT4 mRNA stability and promoted FUT4 translation. qPCR validation of FUT4 enrichment versus input after RP11 RNA pull down using different specific probes as compared to a non-specific one in (A) U-CH1 and (B) JHC7 cells. The stability of FUT4 in transfected (C) U-CH1 and (D) JHC7 cells was measured by RT-qPCR in the presence of the transcription inhibitor Actinomycin D at the indicated time points. The half-life of FUT4 mRNA (t1/2) was calculated from each experiment shown in the graph. 18S rRNA was conducted as an internal control. (E, F) Sucrose density gradient fractionation and isolation of 40S/60S/80S and polysome cytoplasmic components for analysis, and (G, H) then polysome-fractionated samples analyzed by PCR. (I, J) Relative levels of FUT4 mRNAs in each ribosome fraction were quantified and normalized to RCN2 mRNA and plotted as a percentage of the total. Line 1-6, 40S/60S/80S; Line 7-12, polysome. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Data are from three independent polysome-profiling experiments. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.

    Techniques Used: Transfection, Quantitative RT-PCR, Fractionation, Isolation, Negative Control, shRNA, Sequencing

    RP11-867G2.8 modulated FUT4 expression by recruiting EIF4B and PABPC1. (A) RNA pull-down suggested that RP11 bound to EIF4B and PABPC1 in U-CH1 and JHC7 cells. RNA immunoprecipitation experiment using antibodies against EIF4B and PABPC1 to immunoprecipitate RP11-867G2.8 from extracts of (B) U-CH1 and (C) JHC7 cells, followed by qRT-PCR quantification. (D) qRT-PCR and (E) Western blot analysis for FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.
    Figure Legend Snippet: RP11-867G2.8 modulated FUT4 expression by recruiting EIF4B and PABPC1. (A) RNA pull-down suggested that RP11 bound to EIF4B and PABPC1 in U-CH1 and JHC7 cells. RNA immunoprecipitation experiment using antibodies against EIF4B and PABPC1 to immunoprecipitate RP11-867G2.8 from extracts of (B) U-CH1 and (C) JHC7 cells, followed by qRT-PCR quantification. (D) qRT-PCR and (E) Western blot analysis for FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.

    Techniques Used: Expressing, Immunoprecipitation, Quantitative RT-PCR, Western Blot, Transfection, Negative Control, shRNA, Sequencing

    RP11-867G2.8 promoted the malignant phenotype of chordoma cells via FUT4. MTT assay showing the cell proliferation of (A) U-CH1 cells and (B) JHC7 cells transfected with the indicated plasmids. Colony formation of (C) U-CH1 cells and (D) JHC7 cells with different treatments. The transwell assay results demonstrated the migratory activities of (E) U-CH1 and (F) JHC7 cells transfected with the indicated plasmids. Epithelial-mesenchymal transition (EMT) related markers vimentin and N-cadherin in (G) U-CH1 and (H) JHC7 cells transfected with the indicated plasmids were detected by Western blot. NC, negative control; RP11, full sequence of RP11-867G2.8; shFUT4, short-hairpin RNA targeting FUT4. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.
    Figure Legend Snippet: RP11-867G2.8 promoted the malignant phenotype of chordoma cells via FUT4. MTT assay showing the cell proliferation of (A) U-CH1 cells and (B) JHC7 cells transfected with the indicated plasmids. Colony formation of (C) U-CH1 cells and (D) JHC7 cells with different treatments. The transwell assay results demonstrated the migratory activities of (E) U-CH1 and (F) JHC7 cells transfected with the indicated plasmids. Epithelial-mesenchymal transition (EMT) related markers vimentin and N-cadherin in (G) U-CH1 and (H) JHC7 cells transfected with the indicated plasmids were detected by Western blot. NC, negative control; RP11, full sequence of RP11-867G2.8; shFUT4, short-hairpin RNA targeting FUT4. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.

    Techniques Used: MTT Assay, Transfection, Transwell Assay, Western Blot, Negative Control, Sequencing, shRNA

    jhc7  (ATCC)


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    ATCC jhc7
    RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and <t>JHC7)</t> by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.
    Jhc7, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    jhc7 - by Bioz Stars, 2024-05
    99/100 stars

    Images

    1) Product Images from "RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation"

    Article Title: RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation

    Journal: American Journal of Cancer Research

    doi:

    RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and JHC7) by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.
    Figure Legend Snippet: RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and JHC7) by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.

    Techniques Used: Expressing, Quantitative RT-PCR, Fluorescence, In Situ Hybridization, MTT Assay, Transwell Assay, Migration

    FUT4 was high expressed in chordoma tissues, and RP11-867G2.8 promoted the transcription of FUT4. (A) Western blot showing the protein expression of FUT4 in chordoma tissues and normal nucleus pulposus tissues. (B) Western blot showing the protein expression of FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. Expression of FUT4 mRNA in (C) U-CH1 and (D) JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.
    Figure Legend Snippet: FUT4 was high expressed in chordoma tissues, and RP11-867G2.8 promoted the transcription of FUT4. (A) Western blot showing the protein expression of FUT4 in chordoma tissues and normal nucleus pulposus tissues. (B) Western blot showing the protein expression of FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. Expression of FUT4 mRNA in (C) U-CH1 and (D) JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.

    Techniques Used: Western Blot, Expressing, Transfection, Negative Control, shRNA, Sequencing

    RP11-867G2.8 increased FUT4 mRNA stability and promoted FUT4 translation. qPCR validation of FUT4 enrichment versus input after RP11 RNA pull down using different specific probes as compared to a non-specific one in (A) U-CH1 and (B) JHC7 cells. The stability of FUT4 in transfected (C) U-CH1 and (D) JHC7 cells was measured by RT-qPCR in the presence of the transcription inhibitor Actinomycin D at the indicated time points. The half-life of FUT4 mRNA (t1/2) was calculated from each experiment shown in the graph. 18S rRNA was conducted as an internal control. (E, F) Sucrose density gradient fractionation and isolation of 40S/60S/80S and polysome cytoplasmic components for analysis, and (G, H) then polysome-fractionated samples analyzed by PCR. (I, J) Relative levels of FUT4 mRNAs in each ribosome fraction were quantified and normalized to RCN2 mRNA and plotted as a percentage of the total. Line 1-6, 40S/60S/80S; Line 7-12, polysome. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Data are from three independent polysome-profiling experiments. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.
    Figure Legend Snippet: RP11-867G2.8 increased FUT4 mRNA stability and promoted FUT4 translation. qPCR validation of FUT4 enrichment versus input after RP11 RNA pull down using different specific probes as compared to a non-specific one in (A) U-CH1 and (B) JHC7 cells. The stability of FUT4 in transfected (C) U-CH1 and (D) JHC7 cells was measured by RT-qPCR in the presence of the transcription inhibitor Actinomycin D at the indicated time points. The half-life of FUT4 mRNA (t1/2) was calculated from each experiment shown in the graph. 18S rRNA was conducted as an internal control. (E, F) Sucrose density gradient fractionation and isolation of 40S/60S/80S and polysome cytoplasmic components for analysis, and (G, H) then polysome-fractionated samples analyzed by PCR. (I, J) Relative levels of FUT4 mRNAs in each ribosome fraction were quantified and normalized to RCN2 mRNA and plotted as a percentage of the total. Line 1-6, 40S/60S/80S; Line 7-12, polysome. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Data are from three independent polysome-profiling experiments. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.

    Techniques Used: Transfection, Quantitative RT-PCR, Fractionation, Isolation, Negative Control, shRNA, Sequencing

    RP11-867G2.8 modulated FUT4 expression by recruiting EIF4B and PABPC1. (A) RNA pull-down suggested that RP11 bound to EIF4B and PABPC1 in U-CH1 and JHC7 cells. RNA immunoprecipitation experiment using antibodies against EIF4B and PABPC1 to immunoprecipitate RP11-867G2.8 from extracts of (B) U-CH1 and (C) JHC7 cells, followed by qRT-PCR quantification. (D) qRT-PCR and (E) Western blot analysis for FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.
    Figure Legend Snippet: RP11-867G2.8 modulated FUT4 expression by recruiting EIF4B and PABPC1. (A) RNA pull-down suggested that RP11 bound to EIF4B and PABPC1 in U-CH1 and JHC7 cells. RNA immunoprecipitation experiment using antibodies against EIF4B and PABPC1 to immunoprecipitate RP11-867G2.8 from extracts of (B) U-CH1 and (C) JHC7 cells, followed by qRT-PCR quantification. (D) qRT-PCR and (E) Western blot analysis for FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.

    Techniques Used: Expressing, Immunoprecipitation, Quantitative RT-PCR, Western Blot, Transfection, Negative Control, shRNA, Sequencing

    RP11-867G2.8 promoted the malignant phenotype of chordoma cells via FUT4. MTT assay showing the cell proliferation of (A) U-CH1 cells and (B) JHC7 cells transfected with the indicated plasmids. Colony formation of (C) U-CH1 cells and (D) JHC7 cells with different treatments. The transwell assay results demonstrated the migratory activities of (E) U-CH1 and (F) JHC7 cells transfected with the indicated plasmids. Epithelial-mesenchymal transition (EMT) related markers vimentin and N-cadherin in (G) U-CH1 and (H) JHC7 cells transfected with the indicated plasmids were detected by Western blot. NC, negative control; RP11, full sequence of RP11-867G2.8; shFUT4, short-hairpin RNA targeting FUT4. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.
    Figure Legend Snippet: RP11-867G2.8 promoted the malignant phenotype of chordoma cells via FUT4. MTT assay showing the cell proliferation of (A) U-CH1 cells and (B) JHC7 cells transfected with the indicated plasmids. Colony formation of (C) U-CH1 cells and (D) JHC7 cells with different treatments. The transwell assay results demonstrated the migratory activities of (E) U-CH1 and (F) JHC7 cells transfected with the indicated plasmids. Epithelial-mesenchymal transition (EMT) related markers vimentin and N-cadherin in (G) U-CH1 and (H) JHC7 cells transfected with the indicated plasmids were detected by Western blot. NC, negative control; RP11, full sequence of RP11-867G2.8; shFUT4, short-hairpin RNA targeting FUT4. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.

    Techniques Used: MTT Assay, Transfection, Transwell Assay, Western Blot, Negative Control, Sequencing, shRNA

    jhc7 cells  (ATCC)


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    ATCC jhc7 cells
    Jhc7 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/jhc7 cells/product/ATCC
    Average 99 stars, based on 1 article reviews
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    jhc7  (ATCC)


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    ATCC jhc7
    Effects of lncRNA KRT8P41 on chordoma cell malignant behaviors (A) The silencing of lncRNA KRT8P41 in two chordoma cell lines, U-CH1 and <t>JHC7,</t> was achieved by transfecting si-KRT8P41#1/2. The transfection efficiency was verified using real-time qPCR, and si-KRT8P41#1 was used in further experiments because of better efficiency. Then, these two chordoma cell lines were transfected with si-KRT8P41 and examined for (B and C) cell viability by MTT assay; (D) DNA synthesis capacity by EdU assay; (E) colony formation capacity by Colony formation assay; (F) cell invasion by Transwell assay. ** P < 0.01.
    Jhc7, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Long non-coding RNA KRT8P41/miR-193a-3p/FUBP1 axis modulates the proliferation and invasion of chordoma cells"

    Article Title: Long non-coding RNA KRT8P41/miR-193a-3p/FUBP1 axis modulates the proliferation and invasion of chordoma cells

    Journal: Journal of Bone Oncology

    doi: 10.1016/j.jbo.2021.100392

    Effects of lncRNA KRT8P41 on chordoma cell malignant behaviors (A) The silencing of lncRNA KRT8P41 in two chordoma cell lines, U-CH1 and JHC7, was achieved by transfecting si-KRT8P41#1/2. The transfection efficiency was verified using real-time qPCR, and si-KRT8P41#1 was used in further experiments because of better efficiency. Then, these two chordoma cell lines were transfected with si-KRT8P41 and examined for (B and C) cell viability by MTT assay; (D) DNA synthesis capacity by EdU assay; (E) colony formation capacity by Colony formation assay; (F) cell invasion by Transwell assay. ** P < 0.01.
    Figure Legend Snippet: Effects of lncRNA KRT8P41 on chordoma cell malignant behaviors (A) The silencing of lncRNA KRT8P41 in two chordoma cell lines, U-CH1 and JHC7, was achieved by transfecting si-KRT8P41#1/2. The transfection efficiency was verified using real-time qPCR, and si-KRT8P41#1 was used in further experiments because of better efficiency. Then, these two chordoma cell lines were transfected with si-KRT8P41 and examined for (B and C) cell viability by MTT assay; (D) DNA synthesis capacity by EdU assay; (E) colony formation capacity by Colony formation assay; (F) cell invasion by Transwell assay. ** P < 0.01.

    Techniques Used: Transfection, MTT Assay, DNA Synthesis, EdU Assay, Colony Assay, Transwell Assay

    Selection of miRNA negatively correlated to FUBP1 and lncRNA KRT8P41 (A-B) U-CH1 and JHC7 cells were transfected with si-KRT8P41 and examined for FUBP1 protein levels using Immunoblotting. (C) Online tool miRCode ( http://www.mircode.org/ ) was used to predict miRNAs that could target FUBP1 and lncRNA KRT8P41, and the following miRNAs were found: miR-193/193b/193a-3p, miR-192/215, miR-183, miR-338/338-3p, miR-216b/216b-5p, miR-29abcd, and miR-216a. (D) miRNAs differentially expressed in chordoma and non-cancerous tissues according to GSE56183 were shown. These two steps intersected at miR-193a. (E) miR-193a overexpression or inhibition was achieved in U-CH1, and JHC7 cells by transfecting miR-193a mimics/inhibitor. The transfection efficiency was verified using real-time qPCR. (F) U-CH1 and JHC7 cells were transfected with si-KRT8P41 and examined for miR-193a expression using real-time qPCR. (G and H) U-CH1 and JHC7 cells were transfected with miR-193a mimics/inhibitor and examined for FUBP1 protein levels using Immunoblotting. ** P < 0.01.
    Figure Legend Snippet: Selection of miRNA negatively correlated to FUBP1 and lncRNA KRT8P41 (A-B) U-CH1 and JHC7 cells were transfected with si-KRT8P41 and examined for FUBP1 protein levels using Immunoblotting. (C) Online tool miRCode ( http://www.mircode.org/ ) was used to predict miRNAs that could target FUBP1 and lncRNA KRT8P41, and the following miRNAs were found: miR-193/193b/193a-3p, miR-192/215, miR-183, miR-338/338-3p, miR-216b/216b-5p, miR-29abcd, and miR-216a. (D) miRNAs differentially expressed in chordoma and non-cancerous tissues according to GSE56183 were shown. These two steps intersected at miR-193a. (E) miR-193a overexpression or inhibition was achieved in U-CH1, and JHC7 cells by transfecting miR-193a mimics/inhibitor. The transfection efficiency was verified using real-time qPCR. (F) U-CH1 and JHC7 cells were transfected with si-KRT8P41 and examined for miR-193a expression using real-time qPCR. (G and H) U-CH1 and JHC7 cells were transfected with miR-193a mimics/inhibitor and examined for FUBP1 protein levels using Immunoblotting. ** P < 0.01.

    Techniques Used: Selection, Transfection, Western Blot, Over Expression, Inhibition, Expressing

    LncRNA KRT8P41/miR-193a axis modulates chordoma cell aggressiveness through FUBP1 U-CH1 and JHC7 cells were co-transfected with miR-193a inhibitor and si-KRT8P41 and examined for (A and B) cell viability by MTT assay; (C) cell invasion by Transwell assay; (D and E) the protein levels of FUBP1 and c-Myc by Immunoblotting. ** P < 0.01, compared with the control group; ## P < 0.01, compared with the si-NC + miR-193a inhibitor group.
    Figure Legend Snippet: LncRNA KRT8P41/miR-193a axis modulates chordoma cell aggressiveness through FUBP1 U-CH1 and JHC7 cells were co-transfected with miR-193a inhibitor and si-KRT8P41 and examined for (A and B) cell viability by MTT assay; (C) cell invasion by Transwell assay; (D and E) the protein levels of FUBP1 and c-Myc by Immunoblotting. ** P < 0.01, compared with the control group; ## P < 0.01, compared with the si-NC + miR-193a inhibitor group.

    Techniques Used: Transfection, MTT Assay, Transwell Assay, Western Blot

    jhc7 cells  (ATCC)


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    ATCC jhc7 cells
    Effects of lncRNA KRT8P41 on chordoma cell malignant behaviors (A) The silencing of lncRNA KRT8P41 in two chordoma cell lines, U-CH1 and <t>JHC7,</t> was achieved by transfecting si-KRT8P41#1/2. The transfection efficiency was verified using real-time qPCR, and si-KRT8P41#1 was used in further experiments because of better efficiency. Then, these two chordoma cell lines were transfected with si-KRT8P41 and examined for (B and C) cell viability by MTT assay; (D) DNA synthesis capacity by EdU assay; (E) colony formation capacity by Colony formation assay; (F) cell invasion by Transwell assay. ** P < 0.01.
    Jhc7 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Long non-coding RNA KRT8P41/miR-193a-3p/FUBP1 axis modulates the proliferation and invasion of chordoma cells"

    Article Title: Long non-coding RNA KRT8P41/miR-193a-3p/FUBP1 axis modulates the proliferation and invasion of chordoma cells

    Journal: Journal of Bone Oncology

    doi: 10.1016/j.jbo.2021.100392

    Effects of lncRNA KRT8P41 on chordoma cell malignant behaviors (A) The silencing of lncRNA KRT8P41 in two chordoma cell lines, U-CH1 and JHC7, was achieved by transfecting si-KRT8P41#1/2. The transfection efficiency was verified using real-time qPCR, and si-KRT8P41#1 was used in further experiments because of better efficiency. Then, these two chordoma cell lines were transfected with si-KRT8P41 and examined for (B and C) cell viability by MTT assay; (D) DNA synthesis capacity by EdU assay; (E) colony formation capacity by Colony formation assay; (F) cell invasion by Transwell assay. ** P < 0.01.
    Figure Legend Snippet: Effects of lncRNA KRT8P41 on chordoma cell malignant behaviors (A) The silencing of lncRNA KRT8P41 in two chordoma cell lines, U-CH1 and JHC7, was achieved by transfecting si-KRT8P41#1/2. The transfection efficiency was verified using real-time qPCR, and si-KRT8P41#1 was used in further experiments because of better efficiency. Then, these two chordoma cell lines were transfected with si-KRT8P41 and examined for (B and C) cell viability by MTT assay; (D) DNA synthesis capacity by EdU assay; (E) colony formation capacity by Colony formation assay; (F) cell invasion by Transwell assay. ** P < 0.01.

    Techniques Used: Transfection, MTT Assay, DNA Synthesis, EdU Assay, Colony Assay, Transwell Assay

    Selection of miRNA negatively correlated to FUBP1 and lncRNA KRT8P41 (A-B) U-CH1 and JHC7 cells were transfected with si-KRT8P41 and examined for FUBP1 protein levels using Immunoblotting. (C) Online tool miRCode ( http://www.mircode.org/ ) was used to predict miRNAs that could target FUBP1 and lncRNA KRT8P41, and the following miRNAs were found: miR-193/193b/193a-3p, miR-192/215, miR-183, miR-338/338-3p, miR-216b/216b-5p, miR-29abcd, and miR-216a. (D) miRNAs differentially expressed in chordoma and non-cancerous tissues according to GSE56183 were shown. These two steps intersected at miR-193a. (E) miR-193a overexpression or inhibition was achieved in U-CH1, and JHC7 cells by transfecting miR-193a mimics/inhibitor. The transfection efficiency was verified using real-time qPCR. (F) U-CH1 and JHC7 cells were transfected with si-KRT8P41 and examined for miR-193a expression using real-time qPCR. (G and H) U-CH1 and JHC7 cells were transfected with miR-193a mimics/inhibitor and examined for FUBP1 protein levels using Immunoblotting. ** P < 0.01.
    Figure Legend Snippet: Selection of miRNA negatively correlated to FUBP1 and lncRNA KRT8P41 (A-B) U-CH1 and JHC7 cells were transfected with si-KRT8P41 and examined for FUBP1 protein levels using Immunoblotting. (C) Online tool miRCode ( http://www.mircode.org/ ) was used to predict miRNAs that could target FUBP1 and lncRNA KRT8P41, and the following miRNAs were found: miR-193/193b/193a-3p, miR-192/215, miR-183, miR-338/338-3p, miR-216b/216b-5p, miR-29abcd, and miR-216a. (D) miRNAs differentially expressed in chordoma and non-cancerous tissues according to GSE56183 were shown. These two steps intersected at miR-193a. (E) miR-193a overexpression or inhibition was achieved in U-CH1, and JHC7 cells by transfecting miR-193a mimics/inhibitor. The transfection efficiency was verified using real-time qPCR. (F) U-CH1 and JHC7 cells were transfected with si-KRT8P41 and examined for miR-193a expression using real-time qPCR. (G and H) U-CH1 and JHC7 cells were transfected with miR-193a mimics/inhibitor and examined for FUBP1 protein levels using Immunoblotting. ** P < 0.01.

    Techniques Used: Selection, Transfection, Western Blot, Over Expression, Inhibition, Expressing

    LncRNA KRT8P41/miR-193a axis modulates chordoma cell aggressiveness through FUBP1 U-CH1 and JHC7 cells were co-transfected with miR-193a inhibitor and si-KRT8P41 and examined for (A and B) cell viability by MTT assay; (C) cell invasion by Transwell assay; (D and E) the protein levels of FUBP1 and c-Myc by Immunoblotting. ** P < 0.01, compared with the control group; ## P < 0.01, compared with the si-NC + miR-193a inhibitor group.
    Figure Legend Snippet: LncRNA KRT8P41/miR-193a axis modulates chordoma cell aggressiveness through FUBP1 U-CH1 and JHC7 cells were co-transfected with miR-193a inhibitor and si-KRT8P41 and examined for (A and B) cell viability by MTT assay; (C) cell invasion by Transwell assay; (D and E) the protein levels of FUBP1 and c-Myc by Immunoblotting. ** P < 0.01, compared with the control group; ## P < 0.01, compared with the si-NC + miR-193a inhibitor group.

    Techniques Used: Transfection, MTT Assay, Transwell Assay, Western Blot

    jhc7 cells  (ATCC)


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    ATCC jhc7 cells
    CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of <t>JHC7-MOCK</t> and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments
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    1) Product Images from "CMTM3 suppresses chordoma progress through EGFR/STAT3 regulated EMT and TP53 signaling pathway"

    Article Title: CMTM3 suppresses chordoma progress through EGFR/STAT3 regulated EMT and TP53 signaling pathway

    Journal: Cancer Cell International

    doi: 10.1186/s12935-021-02159-5

    CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of JHC7-MOCK and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments
    Figure Legend Snippet: CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of JHC7-MOCK and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Western Blot, Transfection

    68 upregulated and 18 downregulated genes in  JHC7-CMTM3  cells vs. JHC7-MOCK cells (padj < 0.001)
    Figure Legend Snippet: 68 upregulated and 18 downregulated genes in JHC7-CMTM3 cells vs. JHC7-MOCK cells (padj < 0.001)

    Techniques Used: Binding Assay, Activity Assay, Sequencing, Activation Assay

    jhc7 cell lines  (ATCC)


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    ATCC jhc7 cell lines
    CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of <t>JHC7-MOCK</t> and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments
    Jhc7 Cell Lines, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "CMTM3 suppresses chordoma progress through EGFR/STAT3 regulated EMT and TP53 signaling pathway"

    Article Title: CMTM3 suppresses chordoma progress through EGFR/STAT3 regulated EMT and TP53 signaling pathway

    Journal: Cancer Cell International

    doi: 10.1186/s12935-021-02159-5

    CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of JHC7-MOCK and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments
    Figure Legend Snippet: CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of JHC7-MOCK and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Western Blot, Transfection

    68 upregulated and 18 downregulated genes in  JHC7-CMTM3  cells vs. JHC7-MOCK cells (padj < 0.001)
    Figure Legend Snippet: 68 upregulated and 18 downregulated genes in JHC7-CMTM3 cells vs. JHC7-MOCK cells (padj < 0.001)

    Techniques Used: Binding Assay, Activity Assay, Sequencing, Activation Assay

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    ATCC jhc7 cells
    Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines <t>JHC7</t> and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.
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    ATCC human chordoma cell lines jhc7
    Summary of clinical information of <t> chordoma </t> tumor samples and classification.
    Human Chordoma Cell Lines Jhc7, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    jhc7  (ATCC)
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    ATCC jhc7
    RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and <t>JHC7)</t> by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.
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    ATCC jhc7 cell lines
    CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of <t>JHC7-MOCK</t> and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments
    Jhc7 Cell Lines, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.

    Article Snippet: JHC7 cells were cultured in DMEM: F12 medium (ATCC ® 30-2006™, ATCC, USA) and U-CH1 cells were cultured in RPMI-1640 medium (11875093, Gibco, US) supplemented with an additional 1% L-glutamine (25030081, Gibco, US).

    Techniques: Transfection, Western Blot, Negative Control

    Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.

    Article Snippet: JHC7 cells were cultured in DMEM: F12 medium (ATCC ® 30-2006™, ATCC, USA) and U-CH1 cells were cultured in RPMI-1640 medium (11875093, Gibco, US) supplemented with an additional 1% L-glutamine (25030081, Gibco, US).

    Techniques: CCK-8 Assay, Proliferation Assay

    Summary of clinical information of  chordoma  tumor samples and classification.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: Summary of clinical information of chordoma tumor samples and classification.

    Article Snippet: Human chordoma cell lines JHC7 and U-CH1 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques:

    Characterization of the proteome and phosphoproteome in chordoma tumor and normal tissues. (A) General pipeline of (phospho)peptide enrichment and the quantitative mass spectrometric protocol followed by pathway analyses and biochemical validation. (B, C) Principal component analysis (PCA) of the quantified proteome (B) and quantified phosphoproteome (C) . (D, E) Statistical analysis of the 4D label-free proteomic (D) and phosphoproteomic (E) datasets.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: Characterization of the proteome and phosphoproteome in chordoma tumor and normal tissues. (A) General pipeline of (phospho)peptide enrichment and the quantitative mass spectrometric protocol followed by pathway analyses and biochemical validation. (B, C) Principal component analysis (PCA) of the quantified proteome (B) and quantified phosphoproteome (C) . (D, E) Statistical analysis of the 4D label-free proteomic (D) and phosphoproteomic (E) datasets.

    Article Snippet: Human chordoma cell lines JHC7 and U-CH1 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques:

    Targeted proteomic study and altered expression of Wnt-signaling-related proteins. (A) Statistical comparison of regulated proteins between chordoma tissues (CT) and their paired normal adjacent muscle tissues (CN) by Q category. Q1, 0 < ratio ≤ 0.5, corresponding to downregulated proteins; Q2, 0.5 < ratio ≤ 0.667; Q3, 1.5 < ratio ≤ 2; Q4, ratio >2, corresponding to upregulated proteins. Protein numbers for Q1-Q4 are 364/35/171/775, respectively. (B) Volcano plot of the distributional patterns of statistical significance (-log P value) and magnitude of the changes (log 2 FC) for all DEPs. (C) Unsupervised hierarchical clustering heatmap of the significantly regulated proteins identified from chordoma tissues. Unique proteins (n=1,139; rows) were significantly identified from nine paired samples (columns). TP, tumor proteins; NP, normal proteins. Unsupervised hierarchical clustering was performed using the Cluster program with Pearson correlation and pairwise complete-linkage analyses. (D) KEGG pathway-enrichment analysis was executed to identify important pathways that depended upon all DEPs. The colored blocks that correspond to functional classification indicate the magnitude of enrichment, and are displayed by colors ranging from blue (weak enrichment) to red (strong enrichment). (E–N) Relative normalized expression of CTNNB1 (E) , RUVBL1 (F) , RAC1 (G) , RAC2 (H) , RHOA (I) , ROCK2 (J) , PRKACA (K) , CAMK2G (L) , CAMK2D (M) , and CAMK2B (N) . The vertical axis signifies log (2). CN, blue; CT, red. Student’s paired t-test was applied to distinguish the expression differences; *, p < 0.05, **, p < 0.01, ***, p < 0.001.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: Targeted proteomic study and altered expression of Wnt-signaling-related proteins. (A) Statistical comparison of regulated proteins between chordoma tissues (CT) and their paired normal adjacent muscle tissues (CN) by Q category. Q1, 0 < ratio ≤ 0.5, corresponding to downregulated proteins; Q2, 0.5 < ratio ≤ 0.667; Q3, 1.5 < ratio ≤ 2; Q4, ratio >2, corresponding to upregulated proteins. Protein numbers for Q1-Q4 are 364/35/171/775, respectively. (B) Volcano plot of the distributional patterns of statistical significance (-log P value) and magnitude of the changes (log 2 FC) for all DEPs. (C) Unsupervised hierarchical clustering heatmap of the significantly regulated proteins identified from chordoma tissues. Unique proteins (n=1,139; rows) were significantly identified from nine paired samples (columns). TP, tumor proteins; NP, normal proteins. Unsupervised hierarchical clustering was performed using the Cluster program with Pearson correlation and pairwise complete-linkage analyses. (D) KEGG pathway-enrichment analysis was executed to identify important pathways that depended upon all DEPs. The colored blocks that correspond to functional classification indicate the magnitude of enrichment, and are displayed by colors ranging from blue (weak enrichment) to red (strong enrichment). (E–N) Relative normalized expression of CTNNB1 (E) , RUVBL1 (F) , RAC1 (G) , RAC2 (H) , RHOA (I) , ROCK2 (J) , PRKACA (K) , CAMK2G (L) , CAMK2D (M) , and CAMK2B (N) . The vertical axis signifies log (2). CN, blue; CT, red. Student’s paired t-test was applied to distinguish the expression differences; *, p < 0.05, **, p < 0.01, ***, p < 0.001.

    Article Snippet: Human chordoma cell lines JHC7 and U-CH1 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques: Expressing, Functional Assay

    KiPNA analysis and the expression validation of specific proteins. (A) Kinase-pathway network analysis (KiPNA) indicating the proteomic and phosphoproteomic signaling network in chordoma. (B) Fourteen and 29 kinases were conjectured to be negatively and positively regulated, respectively. (C) The elevated expression of brachyury-T, AURA, MOK, and CDK9 were verified by western immunoblotting analysis. The samples were derived from six independent patients who were distinct from the patients whose samples were used for mass spectrometry. T, tumor tissues; N, normal tissues. (D) Densitometric quantification of western blot results from (B) and presented relative to β-actin expression. The data represent the mean ± SD of each experiment carried out in triplicate.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: KiPNA analysis and the expression validation of specific proteins. (A) Kinase-pathway network analysis (KiPNA) indicating the proteomic and phosphoproteomic signaling network in chordoma. (B) Fourteen and 29 kinases were conjectured to be negatively and positively regulated, respectively. (C) The elevated expression of brachyury-T, AURA, MOK, and CDK9 were verified by western immunoblotting analysis. The samples were derived from six independent patients who were distinct from the patients whose samples were used for mass spectrometry. T, tumor tissues; N, normal tissues. (D) Densitometric quantification of western blot results from (B) and presented relative to β-actin expression. The data represent the mean ± SD of each experiment carried out in triplicate.

    Article Snippet: Human chordoma cell lines JHC7 and U-CH1 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques: Expressing, Western Blot, Derivative Assay, Mass Spectrometry

    Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: Knockdown of AURA, MOK, and CDK9 compromises chordoma cell line proliferation. The human chordoma cell lines JHC7 and U-CH1 were used to evaluate the proliferative effects of kinases. (A–C) The efficiency of siRNA-knockdown transfection was confirmed by western blotting of whole-cell extracts from JHC7 cells for AURA (A) , CDK9 (B) , and MOK (C) . si-NC, negative control; si-1 and si-2, two independent siRNAs. (D–F) Densitometric quantification of western blot results from (A–C) . Student’s t-test was used. (G–L) Cellular proliferation after siRNA transfection was quantified by CCK8 assays. Cell growth of JHC7 (G–I) and U-CH1cell lines (J–L) was significantly attenuated by knockdown of AURA, CDK9, and MOK. The data were acquired from three biologically and independently repeated experiments (n=3, data are mean ± s.e.m.) ***: P< 0.001.

    Article Snippet: Human chordoma cell lines JHC7 and U-CH1 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques: Transfection, Western Blot, Negative Control

    Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: Dose-dependent treatment of AZD4573 results in cellular proliferation in chordoma cell lines. (A) Structural cartoon representation of CDK9 protein (pdb ID: 6Z45); AZD4573 is depicted as yellow sticks. (B) Chemical structure of AZD4573. (C, D) AZD4573 drug-sensitivity assays. JHC7 (C) and U-CH1 (D) cells were treated with graded concentrations of AZD4573 (from 0.4 nM to 4000 nM) and proliferation was subsequently determined with the CCK-8 cell-proliferation assay.

    Article Snippet: Human chordoma cell lines JHC7 and U-CH1 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques: CCK-8 Assay, Proliferation Assay

    Important proteins and pathways related to chordoma tumor size. (A) Unsupervised hierarchal clustering disclosed differential protein regulation between large and small chordomas. C1/C3/C4/C13 patients belonged to the large (L) group and C2/C5/CC8/C9/C12 to the small (S) group. (B) Combined KEGG pathway-enrichment analyses for both DEPs and DPPs are depicted as bubble charts. (C) Venn diagram of the proteomics and phosphoproteomics analyses for comparisons between L and S. (D) Seven proteins whose phosphorylation levels were augmented in both CT/CN and L/S groups.

    Journal: Frontiers in Oncology

    Article Title: Proteomics and phosphoproteomics of chordoma biopsies reveal alterations in multiple pathways and aberrant kinases activities

    doi: 10.3389/fonc.2022.941046

    Figure Lengend Snippet: Important proteins and pathways related to chordoma tumor size. (A) Unsupervised hierarchal clustering disclosed differential protein regulation between large and small chordomas. C1/C3/C4/C13 patients belonged to the large (L) group and C2/C5/CC8/C9/C12 to the small (S) group. (B) Combined KEGG pathway-enrichment analyses for both DEPs and DPPs are depicted as bubble charts. (C) Venn diagram of the proteomics and phosphoproteomics analyses for comparisons between L and S. (D) Seven proteins whose phosphorylation levels were augmented in both CT/CN and L/S groups.

    Article Snippet: Human chordoma cell lines JHC7 and U-CH1 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques:

    RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and JHC7) by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.

    Journal: American Journal of Cancer Research

    Article Title: RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation

    doi:

    Figure Lengend Snippet: RP11-867G2.8 promoted the malignant biological behavior of chordoma cells. A. Heat map of the up-regulated and down-regulated lncRNAs with fold change >8. B. Expression of RP11-867G2.8 in chordoma tissues and normal nucleus pulposus tissues (n=12) by qRT-PCR. C. Expression of RP11-867G2.8 in chordoma cell lines (U-CH1, U-CH2, U-CH7 and JHC7) by qRT-PCR. D. Fluorescence in situ hybridization showed that RP11-867G2.8 was simultaneously expressed in the nucleus and cytoplasm of U-CH1 and JHC7 cells. E. We designed three shRNAs to knock down RP11-867G2.8. As indicated by the PCR, the shRNA3 showed the strongest suppressive effect on RP11-867G2.8 expression, followed by the shRNA1. F. MTT assay showed the cell proliferation of U-CH1 cells and JHC7 cells with different treatments. G. Colony formation of U-CH1 cells and JHC7 cells with different treatments. H. The transwell assay results demonstrated the cell migration of the different groups. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001. Bar =10 µm.

    Article Snippet: The chordoma cell lines U-CH1, U-CH2, U-CH7 and JHC7 were purchased from American Type Culture Collection (ATCC, Rockville, MD, USA).

    Techniques: Expressing, Quantitative RT-PCR, Fluorescence, In Situ Hybridization, MTT Assay, Transwell Assay, Migration

    FUT4 was high expressed in chordoma tissues, and RP11-867G2.8 promoted the transcription of FUT4. (A) Western blot showing the protein expression of FUT4 in chordoma tissues and normal nucleus pulposus tissues. (B) Western blot showing the protein expression of FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. Expression of FUT4 mRNA in (C) U-CH1 and (D) JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.

    Journal: American Journal of Cancer Research

    Article Title: RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation

    doi:

    Figure Lengend Snippet: FUT4 was high expressed in chordoma tissues, and RP11-867G2.8 promoted the transcription of FUT4. (A) Western blot showing the protein expression of FUT4 in chordoma tissues and normal nucleus pulposus tissues. (B) Western blot showing the protein expression of FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. Expression of FUT4 mRNA in (C) U-CH1 and (D) JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.

    Article Snippet: The chordoma cell lines U-CH1, U-CH2, U-CH7 and JHC7 were purchased from American Type Culture Collection (ATCC, Rockville, MD, USA).

    Techniques: Western Blot, Expressing, Transfection, Negative Control, shRNA, Sequencing

    RP11-867G2.8 increased FUT4 mRNA stability and promoted FUT4 translation. qPCR validation of FUT4 enrichment versus input after RP11 RNA pull down using different specific probes as compared to a non-specific one in (A) U-CH1 and (B) JHC7 cells. The stability of FUT4 in transfected (C) U-CH1 and (D) JHC7 cells was measured by RT-qPCR in the presence of the transcription inhibitor Actinomycin D at the indicated time points. The half-life of FUT4 mRNA (t1/2) was calculated from each experiment shown in the graph. 18S rRNA was conducted as an internal control. (E, F) Sucrose density gradient fractionation and isolation of 40S/60S/80S and polysome cytoplasmic components for analysis, and (G, H) then polysome-fractionated samples analyzed by PCR. (I, J) Relative levels of FUT4 mRNAs in each ribosome fraction were quantified and normalized to RCN2 mRNA and plotted as a percentage of the total. Line 1-6, 40S/60S/80S; Line 7-12, polysome. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Data are from three independent polysome-profiling experiments. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.

    Journal: American Journal of Cancer Research

    Article Title: RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation

    doi:

    Figure Lengend Snippet: RP11-867G2.8 increased FUT4 mRNA stability and promoted FUT4 translation. qPCR validation of FUT4 enrichment versus input after RP11 RNA pull down using different specific probes as compared to a non-specific one in (A) U-CH1 and (B) JHC7 cells. The stability of FUT4 in transfected (C) U-CH1 and (D) JHC7 cells was measured by RT-qPCR in the presence of the transcription inhibitor Actinomycin D at the indicated time points. The half-life of FUT4 mRNA (t1/2) was calculated from each experiment shown in the graph. 18S rRNA was conducted as an internal control. (E, F) Sucrose density gradient fractionation and isolation of 40S/60S/80S and polysome cytoplasmic components for analysis, and (G, H) then polysome-fractionated samples analyzed by PCR. (I, J) Relative levels of FUT4 mRNAs in each ribosome fraction were quantified and normalized to RCN2 mRNA and plotted as a percentage of the total. Line 1-6, 40S/60S/80S; Line 7-12, polysome. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11-F, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Data are from three independent polysome-profiling experiments. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.

    Article Snippet: The chordoma cell lines U-CH1, U-CH2, U-CH7 and JHC7 were purchased from American Type Culture Collection (ATCC, Rockville, MD, USA).

    Techniques: Transfection, Quantitative RT-PCR, Fractionation, Isolation, Negative Control, shRNA, Sequencing

    RP11-867G2.8 modulated FUT4 expression by recruiting EIF4B and PABPC1. (A) RNA pull-down suggested that RP11 bound to EIF4B and PABPC1 in U-CH1 and JHC7 cells. RNA immunoprecipitation experiment using antibodies against EIF4B and PABPC1 to immunoprecipitate RP11-867G2.8 from extracts of (B) U-CH1 and (C) JHC7 cells, followed by qRT-PCR quantification. (D) qRT-PCR and (E) Western blot analysis for FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.

    Journal: American Journal of Cancer Research

    Article Title: RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation

    doi:

    Figure Lengend Snippet: RP11-867G2.8 modulated FUT4 expression by recruiting EIF4B and PABPC1. (A) RNA pull-down suggested that RP11 bound to EIF4B and PABPC1 in U-CH1 and JHC7 cells. RNA immunoprecipitation experiment using antibodies against EIF4B and PABPC1 to immunoprecipitate RP11-867G2.8 from extracts of (B) U-CH1 and (C) JHC7 cells, followed by qRT-PCR quantification. (D) qRT-PCR and (E) Western blot analysis for FUT4 in U-CH1 and JHC7 cells transfected with the indicated plasmids. NC, negative control; shRP11, short-hairpin RNA targeting RP11-867G2.8; RP11, full sequence of RP11-867G2.8; RP11-O, the overlapping sequence of RP11-867G2.8 with FUT4; RP11-NO, non-overlapping sequence of RP11-867G2.8 with FUT4. Mean ± SD (n=3 independent experiments). ***P<0.001.

    Article Snippet: The chordoma cell lines U-CH1, U-CH2, U-CH7 and JHC7 were purchased from American Type Culture Collection (ATCC, Rockville, MD, USA).

    Techniques: Expressing, Immunoprecipitation, Quantitative RT-PCR, Western Blot, Transfection, Negative Control, shRNA, Sequencing

    RP11-867G2.8 promoted the malignant phenotype of chordoma cells via FUT4. MTT assay showing the cell proliferation of (A) U-CH1 cells and (B) JHC7 cells transfected with the indicated plasmids. Colony formation of (C) U-CH1 cells and (D) JHC7 cells with different treatments. The transwell assay results demonstrated the migratory activities of (E) U-CH1 and (F) JHC7 cells transfected with the indicated plasmids. Epithelial-mesenchymal transition (EMT) related markers vimentin and N-cadherin in (G) U-CH1 and (H) JHC7 cells transfected with the indicated plasmids were detected by Western blot. NC, negative control; RP11, full sequence of RP11-867G2.8; shFUT4, short-hairpin RNA targeting FUT4. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.

    Journal: American Journal of Cancer Research

    Article Title: RP11-867G2.8 promotes EMT and chordoma malignant phenotypes by enhancing FUT4 mRNA stability and translation

    doi:

    Figure Lengend Snippet: RP11-867G2.8 promoted the malignant phenotype of chordoma cells via FUT4. MTT assay showing the cell proliferation of (A) U-CH1 cells and (B) JHC7 cells transfected with the indicated plasmids. Colony formation of (C) U-CH1 cells and (D) JHC7 cells with different treatments. The transwell assay results demonstrated the migratory activities of (E) U-CH1 and (F) JHC7 cells transfected with the indicated plasmids. Epithelial-mesenchymal transition (EMT) related markers vimentin and N-cadherin in (G) U-CH1 and (H) JHC7 cells transfected with the indicated plasmids were detected by Western blot. NC, negative control; RP11, full sequence of RP11-867G2.8; shFUT4, short-hairpin RNA targeting FUT4. Mean ± SD (n=3 independent experiments). *P<0.05, **P<0.01, ***P<0.001.

    Article Snippet: The chordoma cell lines U-CH1, U-CH2, U-CH7 and JHC7 were purchased from American Type Culture Collection (ATCC, Rockville, MD, USA).

    Techniques: MTT Assay, Transfection, Transwell Assay, Western Blot, Negative Control, Sequencing, shRNA

    CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of JHC7-MOCK and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments

    Journal: Cancer Cell International

    Article Title: CMTM3 suppresses chordoma progress through EGFR/STAT3 regulated EMT and TP53 signaling pathway

    doi: 10.1186/s12935-021-02159-5

    Figure Lengend Snippet: CMTM3 induces changes in gene expression profiles. A The number of different expressed genes (padj < 0.05, MOI: 100). B A heat map summary of the gene expression values of JHC7-MOCK and JHC7-CMTM3 cells. Red indicates high and green indicates low gene expression values (padj < 0.001). C KEGG enrichment analysis. The TOP seven upregulated signaling pathways are shown of CMTM3-vs-MOCK in JHC7 cells (padj < 0.05). D The expression of TP53 was detected in CMTM3 overexpressed chordoma cell lines by Real-time PCR. E The expression of TP53 was detected in CMTM3 overexpressed JHC7 cells by western blot. F Up, the transfection efficiency of the CMTM3-siRNA was detected in JHC7 cells by western blot. 100 μg of total protein lysates were loaded; Down. the expression of TP53 in CMTM3 silenced JHC7 cells was detected by western blot. Data were representative of three independent experiments

    Article Snippet: Human chordoma U-CH1, MUG-Chor1 and JHC7 cell lines were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Western Blot, Transfection

    68 upregulated and 18 downregulated genes in  JHC7-CMTM3  cells vs. JHC7-MOCK cells (padj < 0.001)

    Journal: Cancer Cell International

    Article Title: CMTM3 suppresses chordoma progress through EGFR/STAT3 regulated EMT and TP53 signaling pathway

    doi: 10.1186/s12935-021-02159-5

    Figure Lengend Snippet: 68 upregulated and 18 downregulated genes in JHC7-CMTM3 cells vs. JHC7-MOCK cells (padj < 0.001)

    Article Snippet: Human chordoma U-CH1, MUG-Chor1 and JHC7 cell lines were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA).

    Techniques: Binding Assay, Activity Assay, Sequencing, Activation Assay