U133 plus 2.0 microarrays

Manufactured by Thermo Fisher Scientific

Sourced in Germany, United States

The U133 Plus 2.0 microarrays are a high-density oligonucleotide array designed to analyze the expression of over 47,000 transcripts and variants. The arrays are manufactured by Thermo Fisher Scientific and are widely used in genomic research applications.

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Lab products found in correlation

Anti cd138 macs microbeads, by Miltenyi Biotec (2 mentions) Automacs, by Miltenyi Biotec (2 mentions) Gcos 1, by Thermo Fisher Scientific (2 mentions) Rneasy kit, by Qiagen (2 mentions) Expression console, by Thermo Fisher Scientific (2 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) Amo 1, by Leibniz Institute DSMZ (1 mentions) Skmm2, by Leibniz Institute DSMZ (1 mentions) U133plus2.0 microarray, by Thermo Fisher Scientific (1 mentions) Fluidics station 400, by Thermo Fisher Scientific (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions) Ingenuity pathway analysis ipa, by Qiagen (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions)

25 protocols using u133 plus 2.0 microarrays

Correlation of Gene Expression and Plasma Cell Proliferation in Multiple Myeloma

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Bone marrow samples were collected after patients’ written informed consent in accordance with the Declaration of Helsinki and institutional research board approval from Montpellier University hospital. Patients’ MM cells were purified using anti-CD138 MACS microbeads (Miltenyi Biotech, Bergisch Gladbach, Germany). RNA and genomic DNA were extracted using Qiagen kits (Qiagen, Hilden, Germany) and their gene expression profile (GEP) obtained using Affymetrix U133 plus 2.0 microarrays as described.^{18 (link)} Plasma cell labeling index (PCLI)^{19 (link)} was investigated using BrdU incorporation and flow cytometry in 101 patients at diagnosis. Correlation between gene expression and PCLI was determined with a Spearman’s test. We used publicly available Affymetrix GEP (Gene Expression Omnibus, accession number GSE2658) of a cohort of 345 purified MM cells from previously untreated patients from the University of Arkansas for Medical Sciences (UAMS, Little Rock, AR), termed in the following UAMS-TT2 cohort. These patients were treated with total therapy 2 including high-dose melphalan (HDM) and autologous stem cell transplant (ASCT).^{20 (link)} We also used Affymetrix data from the total therapy 3 cohort (UAMS-TT3; n=158; E-TABM-1138)^{21 (link)} of 188 relapsed MM patients subsequently treated with bortezomib (GSE9782) from the study by Mulligan et al.^{22 (link)}

Chatonnet F., Pignarre A., Sérandour A.A., Caron G., Avner S., Robert N., Kassambara A., Laurent A., Bizot M., Agirre X., Prosper F., Martin-Subero J.I., Moreaux J., Fest T, & Salbert G. (2020). The hydroxymethylome of multiple myeloma identifies FAM72D as a 1q21 marker linked to proliferation. Haematologica, 105(3), 774-783.

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Gene Expression Analysis of Plasma Cells in Multiple Myeloma

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Specimens were obtained after institutional review board approved by the University of Arkansas for Medical Sciences in accordance with the Declaration of Helsinki. Gene expression analysis of isolated plasma cells (CD138+) from 870 newly diagnosed MM that had been enrolled into our Total Therapy (TT) 3–5 trials^{14 (link),15 (link)}. MM cells were enriched by CD138 immunomagnetic bead selection of mononuclear cells fractions of bone marrow aspirates (autoMACS; Miltenyi Biotec) and purity (≥80%) was assessed with flow cytometry. Gene expression was performed using U133 Plus 2.0 microarrays (Affymetrix) as previously described.^{16 (link)}

Schinke C.D., Bird J.T., Qu P., Yaccoby S., Lyzogubov V.V., Shelton R., Ling W., Boyle E.M., Deshpande S., Byrum S.D., Washam C., Mackintosh S., Stephens O., Thanendrarajan S., Zangari M., Shaughnessy J J.r., Zhan F., Barlogie B., van Rhee F, & Walker B.A. (2021). PHF19 inhibition as a therapeutic target in Multiple Myeloma. Current research in translational medicine, 69(3), 103290.

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Microarray Analysis of CCOC Cell Lines

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RNA of 12 human CCOC cell lines, 10 human CCOC specimen and 10 normal ovarian surface epithelium specimen were extracted and microarray analysis was performed as described protocol [12 (link)]. In brief, following a single strand reverse transcriptase and amplification step, samples were hybridized to Affymetrix U133 Plus 2.0 microarrays. Class comparison in BRB ArrayTools version 3.2.2 software was utilized to identify differentially expressed genes.

Tsang T.Y., Wei W., Itamochi H., Tambouret R, & Birrer M.J. (2017). Integrated genomic analysis of clear cell ovarian cancers identified PRKCI as a potential therapeutic target. Oncotarget, 8(57), 96482-96495.

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Analyzing Cervical Cancer Transcriptome Using Oncomine

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Oncomine is a bioinformatics platform aimed at collecting, standardizing and analyzing cancer transcriptome microarray data (http://www.oncomine.org) [25 (link)]. We used Oncomine 4.5 to analyze the expression of top MRs (CENPF and TOP2A) in different cancers types. All datasets were filtered using the gene symbol, “Analysis Type = Cancer vs. Cancer Analysis” and “Cancer Type = cervical cancer”. The “Bittner Multi-cancer” dataset was returned as the top significant dataset. “Bittner Multi-cancer” is from the Expression Project for Oncology (expO) which contains 1911 various tumor samples analyzed on Affymetrix U133 Plus 2.0 microarrays (unpublished, GEO ID, GSE2109). The log2 median-centered intensity was used as gene expression value. The expression difference of a MR in cervical cancer vs. other cancer types was tested using Student’s t-test.

Yu B., Chen L., Zhang W., Li Y., Zhang Y., Gao Y., Teng X., Zou L., Wang Q., Jia H., Liu X., Zheng H., Hou P., Yu H., Sun Y., Zhang Z., Zhang P, & Zhang L. (2020). TOP2A and CENPF are synergistic master regulators activated in cervical cancer. BMC Medical Genomics, 13, 145.

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Comparative Analysis of Prostate Cancer Transcriptomes

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Gene expression profiles in normal and prostate cancer tissues were assessed using the RNA sequencing (RNA-seq) dataset derived from The Cancer Genome Atlas–Prostate Adenocarcinoma (TCGA-PRAD) project20 (link) as the primary approach to compare gene expression between normal and cancerous tissues. In addition, complementary DNA (cDNA) microarray datasets on the Oncomine online platform21 (link),22 (link),23 (link),24 (link) were also used to verify the RNA-seq data. These cDNA microarray datasets were generated with Affymetrix U133 Plus 2.0 microarrays (Affymetrix, Waltham, MA, USA).
Cell type-specific gene expression in the prostate gland was assessed with the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) dataset GDS1973,25 (link) generated from four different cell types using an antibody pull-down approach against distinct cell surface-specific markers. Immunoprecipitation-pulled down cells were collected for total RNA extracted, followed by RNA-seq analysis.

Huang J., Liu W., Lin B.Y., Li J.C., Lu J, & Li B.Y. (2022). Scaffold protein MAPK8IP2 expression is a robust prognostic factor in prostate cancer associated with AR signaling activity. Asian Journal of Andrology, 25(2), 198-207.

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Evaluating FOXM1 mRNA Levels in Myeloma

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Levels of FOXM1 mRNA in myeloma cells were determined using Affymetrix U133Plus 2.0 microarrays (Santa Clara, CA) as previously described [15 (link), 16 (link)]. Statistical analysis of microarray data relied on GCOS1.1 software (Affymetrix, Santa Clara, CA). Patients at UAMS were treated using the Total Therapy 2 regimen, the backbone of which is high-dose melphalan therapy (HDT) and autologous stem cell transplantation (ASCT). Half of the patients received thalidomide both during intensive therapy and as maintenance therapy. The therapeutic approach to relapsing disease was not uniform and depended mainly on the time to relapse, the pace of relapse (slow versus aggressive), the presence or absence of organ dysfunction, and the patient’s overall health status, physical and mental fitness and treatment preference.

Gu C., Jing X., Holman C., Sompallae R., Zhan F., Tricot G., Yang Y, & Janz S. (2018). Upregulation of FOXM1 leads to diminished drug sensitivity in myeloma. BMC Cancer, 18, 1152.

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Gene Expression Profiling of Multiple Myeloma

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A total of 71 newly diagnosed MM patients screened at the University of Arkansas for Medical Sciences and with simultaneously available information on CD19 and CD81 immunophenotypic patterns of expression and GEP were included in this analysis. An aliquot of BM aspirate was collected to isolate CD138⁺ PCs with immunomagnetic bead selection (autoMACS; Miltenyi Biotec, Bergisch Gladbach, Germany), as described elsewhere.25 (link) Purity of PC was monitored by flow cytometry and was ≥ 85%. Total RNA was used to measure GEP with Affymetrix U133 Plus 2.0 microarrays. Differentially expressed genes between classes were identified using the Significant Analysis of Microarrays algorithm. Analyses were performed using BRB-ArrayTools (version 4.4.1) developed by Dr Richard Simon and the BRB-ArrayTools Development Team, available at http://linus.nci.nih.gov/BRB-ArrayTools.html.

Paiva B., Puig N., Cedena M., de Jong B., Ruiz Y., Rapado I., Martinez-Lopez J., Cordon L., Alignani D., Delgado J., van Zelm M., Van Dongen J., Pascual M., Agirre X., Prosper F., Martín-Subero J., Vidriales M.B., Gutierrez N., Hernandez M., Oriol A., Echeveste M., Gonzalez Y., Johnson S., Epstein J., Barlogie B., Morgan G., Orfao A., Blade J., Mateos M., Lahuerta J, & San-Miguel J. (2016). Differentiation stage of myeloma plasma cells: biological and clinical significance. Leukemia, 31(2), 382-392.

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Obtaining and Authenticating Human Myeloma Cell Lines

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XG HMCLs were obtained as previously described [18 (link)]. JJN3 was kindly provided by Dr. Van Riet (Brussels, Belgium), JIM3 by Dr. MacLennan (Birmingham, UK), and MM1S by Dr. S. Rosen (Chicago, USA). AMO-1, LP1, L363, U266, OPM2, and SKMM2 were purchased from DSMZ (Braunsweig, Germany) and RPMI8226 from ATTC (Rockville, MD, USA). All HMCLs derived in our laboratory were cultured in the presence of recombinant IL-6. HMCLs were authenticated according to their short tandem repeat profiling and their gene expression profiling using Affymetrix U133 plus 2.0 microarrays deposited in the ArrayExpress public database under accession numbers E-TABM-937 and E-TABM-1088 [18 (link)].

Kassambara A., Herviou L., Ovejero S., Jourdan M., Thibaut C., Vikova V., Pasero P., Elemento O, & Moreaux J. (2021). RNA-sequencing data-driven dissection of human plasma cell differentiation reveals new potential transcription regulators. Leukemia, 35(5), 1451-1462.

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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.

Yu J., Li X., Zhong C., Li D., Zhai X., Hu W., Guo C., Yuan Y, & Zheng S. (2016). High-throughput proteomics integrated with gene microarray for discovery of colorectal cancer potential biomarkers. Oncotarget, 7(46), 75279-75292.

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Resveratrol-Induced Transcriptomic Analysis

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After a 6-h treatment with 10 μM resveratrol, cells were collected by trypsinization and total RNA was extracted using the RNeasy kit (Qiagen). Amount and quality of the RNA fractions were evaluated by UV spectrophotometry (260 and 280 nm wavelength) followed by examination of the probes by capillary electrophoresis on Agilent Bioanalyzers. GeneChip expression and IVT (in vitro transcription) labeling kits (Affymetrix, Santa Clara, CA, USA) were used for the synthesis of cDNA and complementary RNA respectively. Biotin-labeled RNA was fragmented and hybridized on human genome U133 plus 2.0 microarrays (Affymetrix) following the manufacturer's instructions. After hybridization (16 h), the microarrays were processed by automated washing on the Affymetrix Fluidics Station 400. Staining of the hybridized probes was performed with fluorescent streptavidin–phycoerythrin conjugates (1 mg/ml; Invitrogen). The scanning of DNA microarrays was carried out on an Affymetrix laser instrument. Microarray quality assessment, condensing of the probe sets, data normalization, and filtering were conducted (Genedata AG, Basel, Switzerland).

Chin Y.T., Hsieh M.T., Yang S.H., Tsai P.W., Wang S.H., Wang C.C., Lee Y.S., Cheng G.Y., HuangFu W.C., London D., Tang H.Y., Fu E., Yen Y., Liu L.F., Lin H.Y, & Davis P.J. (2014). Anti-proliferative and gene expression actions of resveratrol in breast cancer cells in vitro. Oncotarget, 5(24), 12891-12907.

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