U133plus2.0 microarray
Manufactured by Thermo Fisher Scientific
Sourced in United States
The U133Plus2.0 microarray is a laboratory equipment product manufactured by Thermo Fisher Scientific. It is a gene expression microarray designed for the comprehensive analysis of the human genome. The device allows for the measurement and analysis of the expression levels of thousands of genes simultaneously.
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24 protocols using u133plus2.0 microarray
1
Gene Expression Profiling via Affymetrix U133 Plus2.0
2
Gene Expression Profiles in Multiple Myeloma
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Gene expression profiles for 351 patients with MM, 22 patients with NPC, 44 with MGUS, and 12 with SMM were performed using the Affymetrix U133Plus2.0 microarray as previously described [17 (link)]. Microarray data used in this study have been deposited in the NIH Gene Expression Omnibus under accession numbers GSE2658 and GSE5900. Gene expression analysis was performed using Partek Genomic Suite 6.6 with fold changes calculated as relative changes compared to normal plasma cells, with fold-changes of at least 1.5 fold with a p < 0.05 and a FDR < 0.05 were considered for further analysis.
3
Gene Expression Profiling of Multiple Myeloma
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Smoking-related Gene Expression in Airway Epithelium
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Although BC represent only a minority of the total airway epithelium, we assessed gene expression microarrays of the total airway epithelium to see if a similar signal of 19q13.2-relevant smoking-related gene expression might be detected in the complete epithelium. To accomplish this, we used Affymetrix U133 Plus 2.0 microarray of airway epithelium of smokers (n = 31) vs nonsmokers (n = 21) of the same order of bronchi of airway epithelium from which the nonsmoker and smoker BC were derived.
5
Correlating TRAP1 Expression in Ovarian Cancer
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Serous OC cases from Tothill data set (Affymetrix, Santa Clara, CA, USA U133 plus2.0 microarray, GSE9891) and TCGA data set (level 3 data, total RNA sequencing and Reverse Phase Protein Array) were used to correlate TRAP1 mRNA expression with stage, grade and PFS in Figures 1a–c , and to correlate with the expression of other genes in Figure 6c . Wilcoxon rank sum test was used to compare gene expression between two groups. Kruskal–Wallis test with 10 000 permutation was used to compare gene expression among more than two groups. Log-rank test was used to determine the significance of the survival analysis. Pearson's product moment correlation coefficient was used to correlate the mRNA expression of two genes.
The paired Student's t-test was used to establish the statistical significance of differences between gene expression levels in qPCR and between viability/apoptosis/PFK activity levels under TRAP1 silencing or drug treatments. Two-tailed Mann–Whitney test was used to determine statistical significance of metabolic measurements reported inFigure 3 .
The paired Student's t-test was used to establish the statistical significance of differences between gene expression levels in qPCR and between viability/apoptosis/PFK activity levels under TRAP1 silencing or drug treatments. Two-tailed Mann–Whitney test was used to determine statistical significance of metabolic measurements reported in
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Transcriptional profiling of TRPV2 in myeloma
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Gene Expression Omnibus (GEO) data were carried out to examine the expression of transient receptor potential channels in MM patients (GSE24080) and MM cell lines (GSE6205) [19 (link)]. Data acquisition and normalization methods in these datasets have been described previously [19 (link)]. The mRNA expression of TRPV2 (GSE2658) in plasma cells was determined using the Affymetrix U133Plus2.0 microarray (Affymetrix, USA), which were performed as previously described [20 (link)].
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Affymetrix Microarray Protocol for Plasma-Cell Analysis
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GEP using the Affymetrix U133Plus 2.0 microarray (Santa Clara, CA) were performed as previously described [39 (link)]. Microarray data and outcome data on the 351 patients included in this study are available in the NIH Gene Expression Omnibus (GEO) under accession number GSE2658. Microarray data on the 44 individuals with MGUS and 22 samples of normal plasma cells (NPC) included here are available at GSE5900. Plasma-cell isolation, total RNA extraction, cRNA synthesis, and hybridization to microarrays were performed as described previously [18 (link)]. Statistical analysis of microarray data took advantage of the GCOS1.1 software (Affymetrix, Santa Clara, CA) and involved log-rank tests for univariate association with disease-related survival.
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Affymetrix U133plus2.0 Microarray Protocol
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All samples were concurrently analyzed using Affymetrix U133plus2.0 microarrays. The extraction of RNA was performed following standard protocols provided by the manufacturers. For gene expression analysis, tumor and adjacent normal tissues were investigated using an Affymetrix U133plus2.0 microarray. Data were Acquired by GeneChip® Operating SoftwareVersion1.4. After quality checks, raw intensity data were Processed by quantile normalization with Robust Multi-Anlysis (RMA) to remove systematic bias using Affymetrix Expression Console Version 1.12.
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Gene Expression Profiling of HGF in PCs
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Gene expression profiling was performed as previously described using the Affymetrix U133Plus2.0 microarray (Affymetrix, Santa Clara, CA, USA) [19 (link)-22 (link)]. Microarray data of the HGF gene expression profile in PCs isolated from 22 healthy donors (NPC), 14 patients diagnosed with monoclonal gammopathy of undetermined significance (MGUS), 34 patients with smouldering MM (SMM), 344 MM patients and 45 HMCLs were retrieved from the NIH Gene Expression Omnibus17, which can be found under accession number GSE2658. The Mann–Whitney test (two-tailed) was performed for analysis of statistical significance.
10
IRF4 Expression in Plasma Cell Disorders
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Gene Expression Omnibus (GEO) data were carried out to examine the expression of IRF4 in normal plasma (NP), monoclonal gammopathy of undetermined significance (MGUS) (GSE5900), and MM (GSE2658) plasma cells. The plasma cells were determined using the Affymetrix U133Plus2.0 microarray (Affymetrix, USA), which were performed as previously described [33 (link)].
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