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Rosetta Inpharmatics gene expression microarray data set
Gene Expression Microarray Data Set, supplied by Rosetta Inpharmatics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Gene Expression:

Article Title: MammaPrint 70-gene profile quantifies the likelihood of recurrence for early breast cancer.
Article Snippet: Background: Over the past few years, a variety of multigene expression profiles have been developed to improve prognostication for early stage breast cancer and reduce overtreatment with chemotherapy.. MammaPrint is the only test cleared by the US Food and Drug Administration for the prognostication of early breast cancer.. The MammaPrint assay examines the expression of 70 genes in the primary tumor to stratify patients diagnosed with early stage breast cancer into good and poor prognosis groups.

Article Title: Peroxidase-dependent apoplastic oxidative burst in Arabidopsis required for pathogen resistance
Article Snippet: .. 3.2 gene expression data analysis system (Rosetta Inpharmatics, Kirkland, WA, USA), using Affymetrix CEL files of array feature intensities and standard deviations as input. ..

Article Title: Notch1 inhibition alters the CD44 hi /CD24 lo population and reduces the formation of brain metastases from breast cancer
Article Snippet: .. We interrogated a comprehensive gene expression microarray data set of 295 primary breast tumors (obtained from Rosetta Inpharmatics, Seattle, WA, USA) prepared by van de Vijver and colleagues, who used it to identify gene expression signatures predictive of outcome. ..

Article Title: ADAM8 expression in invasive breast cancer promotes tumor dissemination and metastasis
Article Snippet: .. A comprehensive gene expression microarray data set of 295 primary breast tumors (obtained from Rosetta Inpharmatics) prepared by van de Vijver and colleagues (van de Vijver et al , ), was used to compare ADAM8 mRNA levels across the different molecular breast cancer subtypes and to assess its correlation with patient outcome. ..

Article Title: Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.
Article Snippet: Background and aims The incidence of oesophageal adenocarcinoma (OAC) has been increasing rapidly with a dismal survival rate of less than 20%.. Understanding the genomic aberrations and biology of this cancer may enhance disease interventions.. This study aimed to use genome-wide genomic and expression data to enhance the understanding of OAC pathogenesis and identify groups with differential outcomes.

Article Title: Notch1 inhibition alters the CD44 hi /CD24 lo population and reduces the formation of brain metastases from breast cancer
Article Snippet: .. Analysis of a Published Microarray Dataset We interrogated a comprehensive gene expression microarray data set of 295 primary breast tumors (obtained from Rosetta Inpharmatics, Seattle, WA, USA) prepared by van de Vijver and colleagues, who used it to identify gene expression signatures predictive of outcome. ..

Article Title: Mammary differentiation induces expression of Tristetraprolin, a tumor suppressor AU-rich mRNA-binding protein.
Article Snippet: Tristetraprolin (TTP) is a RNA-binding protein that inhibits the expression of pro-inflammatory cytokines and invasiveness-associated genes.. TTP levels are decreased in many different cancer types and it has been proposed that this protein could be used as a prognostic factor in breast cancer.. Here, using publicly available DNA microarray datasets, ‘‘serial analysis of gene expression’’ libraries and qRT-PCR analysis, we determined that TTP mRNA is present in normal breast cells and its levels are significantly decreased in all breast cancer subtypes.

Article Title: Notch1 Inhibition Alters the CD44hi/CD24lo Population and Reduces the Formation of Brain Metastases from Breast Cancer
Article Snippet: .. Analysis of a published microarray data set We interrogated a comprehensive gene expression microarray data set of 295 primary breast tumors (obtained from Rosetta Inpharmatics) prepared by van de Vijver and colleagues, who used it to identify gene expression signatures predictive of outcome. ..

Microarray:

Article Title: Notch1 inhibition alters the CD44 hi /CD24 lo population and reduces the formation of brain metastases from breast cancer
Article Snippet: .. We interrogated a comprehensive gene expression microarray data set of 295 primary breast tumors (obtained from Rosetta Inpharmatics, Seattle, WA, USA) prepared by van de Vijver and colleagues, who used it to identify gene expression signatures predictive of outcome. ..

Article Title: ADAM8 expression in invasive breast cancer promotes tumor dissemination and metastasis
Article Snippet: .. A comprehensive gene expression microarray data set of 295 primary breast tumors (obtained from Rosetta Inpharmatics) prepared by van de Vijver and colleagues (van de Vijver et al , ), was used to compare ADAM8 mRNA levels across the different molecular breast cancer subtypes and to assess its correlation with patient outcome. ..

Article Title: Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.
Article Snippet: Background and aims The incidence of oesophageal adenocarcinoma (OAC) has been increasing rapidly with a dismal survival rate of less than 20%.. Understanding the genomic aberrations and biology of this cancer may enhance disease interventions.. This study aimed to use genome-wide genomic and expression data to enhance the understanding of OAC pathogenesis and identify groups with differential outcomes.

Article Title: Notch1 inhibition alters the CD44 hi /CD24 lo population and reduces the formation of brain metastases from breast cancer
Article Snippet: .. Analysis of a Published Microarray Dataset We interrogated a comprehensive gene expression microarray data set of 295 primary breast tumors (obtained from Rosetta Inpharmatics, Seattle, WA, USA) prepared by van de Vijver and colleagues, who used it to identify gene expression signatures predictive of outcome. ..

Article Title: Notch1 Inhibition Alters the CD44hi/CD24lo Population and Reduces the Formation of Brain Metastases from Breast Cancer
Article Snippet: .. Analysis of a published microarray data set We interrogated a comprehensive gene expression microarray data set of 295 primary breast tumors (obtained from Rosetta Inpharmatics) prepared by van de Vijver and colleagues, who used it to identify gene expression signatures predictive of outcome. ..



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ZEB1-AS1 sponges miR-141-3p in CRC cells. ( A ) Nuclear and cytoplasmic fractionation was analyzed for ZEB1-AS1 expression in SW480 and LOVO. ( B ) The <t>microRNA</t> array analysis in normal and tumor tissues. ( C ) The potential binding sites between ZEB1-AS1 and miR-141-3p. ( D ) The expressions of miR-141-3p in CRC tissues were detected by RT-qPCR. ( E ) Luciferase reporter assay showed ZEB1-AS1-wt activity was impaired by miR-141-3p. ( F ) The expression of miR-141-3p in SW480 and LOVO was upregulated after ZEB1-AS1 expression was downregulated identified by RT-qPCR. ( G ) The expression of miR-141-3p was negatively correlated with ZEB1-AS1 expression in CRC tissues. * P < 0.05.
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ABCG2 upregulation is associated with SIK3 attenuation. (A) List of ABC family proteins from <t>microarray</t> data for which the expression changed more than 1.5-fold compared with control cells. (B) The mRNA expression levels of ABC proteins were verified by real-time PCR in OVCAR4 and SKOV3 cells. The white bar (shLuc) represents control cells, and the gray bar (shSIK3#01) and black bar (shSIK3#61) represent indicated cells with SIK3 knockdown. Data are represented as the mean ± SEM from three independent experiments and analyzed by one-way ANOVA. *: p <0.05 and **: p <0.01 (compared to the shLuc control). Note that ABCG1 and ABCG2 were both significantly upregulated in cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (C) The protein expression levels of ABCG1 and ABCG2 were further verified by Western blotting. Note that only ABCG2 was upregulated in OVCAR4 and SKOV3 cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (D) The functional MDR activity of the ABCG2 protein was determined using an MDR assay kit (Abcam). A total of 2 x 10 5 suspended cells were pretreated with the inhibitor novobiocin (50 nM) or DMSO. Then, diluted Efflux Gold Detection Reagent was added at 37°C for 30 minutes. The cellular orange fluorescence signal of the Efflux Gold Detection Reagent was measured immediately by flow cytometry in the living (PI-negative) cell population. The numbers in the upper left corners are MAF values.
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ABCG2 upregulation is associated with SIK3 attenuation. (A) List of ABC family proteins from <t>microarray</t> data for which the expression changed more than 1.5-fold compared with control cells. (B) The mRNA expression levels of ABC proteins were verified by real-time PCR in OVCAR4 and SKOV3 cells. The white bar (shLuc) represents control cells, and the gray bar (shSIK3#01) and black bar (shSIK3#61) represent indicated cells with SIK3 knockdown. Data are represented as the mean ± SEM from three independent experiments and analyzed by one-way ANOVA. *: p <0.05 and **: p <0.01 (compared to the shLuc control). Note that ABCG1 and ABCG2 were both significantly upregulated in cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (C) The protein expression levels of ABCG1 and ABCG2 were further verified by Western blotting. Note that only ABCG2 was upregulated in OVCAR4 and SKOV3 cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (D) The functional MDR activity of the ABCG2 protein was determined using an MDR assay kit (Abcam). A total of 2 x 10 5 suspended cells were pretreated with the inhibitor novobiocin (50 nM) or DMSO. Then, diluted Efflux Gold Detection Reagent was added at 37°C for 30 minutes. The cellular orange fluorescence signal of the Efflux Gold Detection Reagent was measured immediately by flow cytometry in the living (PI-negative) cell population. The numbers in the upper left corners are MAF values.
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ZEB1-AS1 sponges miR-141-3p in CRC cells. ( A ) Nuclear and cytoplasmic fractionation was analyzed for ZEB1-AS1 expression in SW480 and LOVO. ( B ) The microRNA array analysis in normal and tumor tissues. ( C ) The potential binding sites between ZEB1-AS1 and miR-141-3p. ( D ) The expressions of miR-141-3p in CRC tissues were detected by RT-qPCR. ( E ) Luciferase reporter assay showed ZEB1-AS1-wt activity was impaired by miR-141-3p. ( F ) The expression of miR-141-3p in SW480 and LOVO was upregulated after ZEB1-AS1 expression was downregulated identified by RT-qPCR. ( G ) The expression of miR-141-3p was negatively correlated with ZEB1-AS1 expression in CRC tissues. * P < 0.05.

Journal: International Journal of Medical Sciences

Article Title: Long noncoding RNA ZEB1-AS1 acts as a Sponge of miR-141-3p to Inhibit Cell Proliferation in Colorectal Cancer

doi: 10.7150/ijms.46698

Figure Lengend Snippet: ZEB1-AS1 sponges miR-141-3p in CRC cells. ( A ) Nuclear and cytoplasmic fractionation was analyzed for ZEB1-AS1 expression in SW480 and LOVO. ( B ) The microRNA array analysis in normal and tumor tissues. ( C ) The potential binding sites between ZEB1-AS1 and miR-141-3p. ( D ) The expressions of miR-141-3p in CRC tissues were detected by RT-qPCR. ( E ) Luciferase reporter assay showed ZEB1-AS1-wt activity was impaired by miR-141-3p. ( F ) The expression of miR-141-3p in SW480 and LOVO was upregulated after ZEB1-AS1 expression was downregulated identified by RT-qPCR. ( G ) The expression of miR-141-3p was negatively correlated with ZEB1-AS1 expression in CRC tissues. * P < 0.05.

Article Snippet: Shanghai Biotechnology Co., Ltd conducted the microRNA microarray gene expression experiments and data analysis.

Techniques: Fractionation, Expressing, Binding Assay, Quantitative RT-PCR, Luciferase, Reporter Assay, Activity Assay

ABCG2 upregulation is associated with SIK3 attenuation. (A) List of ABC family proteins from microarray data for which the expression changed more than 1.5-fold compared with control cells. (B) The mRNA expression levels of ABC proteins were verified by real-time PCR in OVCAR4 and SKOV3 cells. The white bar (shLuc) represents control cells, and the gray bar (shSIK3#01) and black bar (shSIK3#61) represent indicated cells with SIK3 knockdown. Data are represented as the mean ± SEM from three independent experiments and analyzed by one-way ANOVA. *: p <0.05 and **: p <0.01 (compared to the shLuc control). Note that ABCG1 and ABCG2 were both significantly upregulated in cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (C) The protein expression levels of ABCG1 and ABCG2 were further verified by Western blotting. Note that only ABCG2 was upregulated in OVCAR4 and SKOV3 cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (D) The functional MDR activity of the ABCG2 protein was determined using an MDR assay kit (Abcam). A total of 2 x 10 5 suspended cells were pretreated with the inhibitor novobiocin (50 nM) or DMSO. Then, diluted Efflux Gold Detection Reagent was added at 37°C for 30 minutes. The cellular orange fluorescence signal of the Efflux Gold Detection Reagent was measured immediately by flow cytometry in the living (PI-negative) cell population. The numbers in the upper left corners are MAF values.

Journal: Journal of Cancer

Article Title: Downregulated Salt-inducible Kinase 3 Expression Promotes Chemoresistance in Serous Ovarian Cancer via the ATP‐binding Cassette Protein ABCG2

doi: 10.7150/jca.34886

Figure Lengend Snippet: ABCG2 upregulation is associated with SIK3 attenuation. (A) List of ABC family proteins from microarray data for which the expression changed more than 1.5-fold compared with control cells. (B) The mRNA expression levels of ABC proteins were verified by real-time PCR in OVCAR4 and SKOV3 cells. The white bar (shLuc) represents control cells, and the gray bar (shSIK3#01) and black bar (shSIK3#61) represent indicated cells with SIK3 knockdown. Data are represented as the mean ± SEM from three independent experiments and analyzed by one-way ANOVA. *: p <0.05 and **: p <0.01 (compared to the shLuc control). Note that ABCG1 and ABCG2 were both significantly upregulated in cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (C) The protein expression levels of ABCG1 and ABCG2 were further verified by Western blotting. Note that only ABCG2 was upregulated in OVCAR4 and SKOV3 cells with SIK3 knocked down by shSIK3#01 and shSIK3#61. (D) The functional MDR activity of the ABCG2 protein was determined using an MDR assay kit (Abcam). A total of 2 x 10 5 suspended cells were pretreated with the inhibitor novobiocin (50 nM) or DMSO. Then, diluted Efflux Gold Detection Reagent was added at 37°C for 30 minutes. The cellular orange fluorescence signal of the Efflux Gold Detection Reagent was measured immediately by flow cytometry in the living (PI-negative) cell population. The numbers in the upper left corners are MAF values.

Article Snippet: TRIzol-isolated RNA samples were shipped on dry ice to Welgene Biotech (Taiwan), where the gene expression microarray experiments were performed as a contract service.

Techniques: Microarray, Expressing, Control, Real-time Polymerase Chain Reaction, Knockdown, Western Blot, Functional Assay, Activity Assay, Fluorescence, Flow Cytometry