Humanwg 6 v3.0 expression beadchip

Manufactured by Illumina

Sourced in United States

The HumanWG-6 v3.0 expression beadchip is a lab equipment product designed for gene expression analysis. It provides a platform for the simultaneous measurement of the expression levels of over 48,000 transcript probes derived from the human genome. The beadchip utilizes bead-based technology to enable high-throughput, genome-wide expression profiling.

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Lab products found in correlation

Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (10 mentions) Beadarray reader, by Illumina (3 mentions) Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (3 mentions) Human gene 1.0 st array, by Thermo Fisher Scientific (3 mentions) Human genome u133 plus 2.0 array, by Illumina (3 mentions) Experion automated electrophoresis system, by Bio-Rad (2 mentions) Beadstudio software, by Illumina (2 mentions) Rneasy plus mini kit, by Qiagen (2 mentions) Iscan system, by Illumina (2 mentions) Human 6 v2 expression beadchip, by Illumina (2 mentions) Human genome u133a array, by Thermo Fisher Scientific (2 mentions) Genomestudio software, by Illumina (1 mentions) Rneasy lipid tissue mini kit, by Qiagen (1 mentions) Beadstudio v3, by Illumina (1 mentions) Cyanin 3 streptavidin, by Cytiva (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions) Infinium humanmethylation27 beadchip, by Illumina (1 mentions) Totalprep 96 rna amplification kit, by Illumina (1 mentions) Genomestudio data analysis software, by Illumina (1 mentions) Streptavidin cy3, by GE Healthcare (1 mentions)

58 protocols using humanwg 6 v3.0 expression beadchip

Transcriptome Profiling of Lung Adenocarcinoma

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Total RNA was extracted from lung adenocarcinoma cell lines using RNeasy Plus Mini Kit (QIAGEN). RNA quality and concentration were checked by the Experion Automated Electrophoresis System (Bio-Rad) according to manufacturer's protocol. Expression data were obtained using the Illumina Human WG-6 v3.0 Expression BeadChips (Illumina) at the Genomics Core at UT Southwestern. Bead-summarized data were obtained using the Illumina BeadStudio software, and pre-processed using the R package MBCB (Model-based Background Correction for Beadarray) for background correction and probe summarization. Pre-processed data were the quantile-normalized and log transformed.

Taguchi A., Delgado O., Çeliktaş M., Katayama H., Wang H., Gazdar A.F, & Hanash S.M. (2014). Proteomic signatures associated with p53 mutational status in lung adenocarcinoma. Proteomics, 14(0), 2750-2759.

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FKBP5 mRNA Expression in BA11

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FKBP5 mRNA was extracted from adjacent blocks of frozen BA11 using Qiagen RNeasy Lipid Tissue Mini Kit and stored at −80°. Whole genome expression analysis using Illumina Human WG-6 v3.0 Expression BeadChips (Illumina Inc, San Diego CA) “direct hybridization” assay was performed on blinded specimens. Arrays were scanned on an Illumina iScan System™ and processed on the Illumina GenomeStudio software. mRNA levels of FKBP5 in all cases were detectable with p < 0.0001.

Young K.A., Thompson P.M., Cruz D.A., Williamson D.E, & Selemon L.D. (2015). BA11 FKBP5 expression levels correlate with dendritic spine density in postmortem PTSD and controls. Neurobiology of Stress, 2, 67-72.

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Illumina Microarray Analysis of Skeletal Muscle

Cited 1 time

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The RNA preparation, cRNA generation and microarray hybridization procedures were used as previously described [24 (link)]. In brief, Trizol-reagent (Invitrogen, Carlsbad, CA, USA) was used to isolate total RNA from the twin muscle biopsies, which were homogenized on FastPrep FP120 apparatus (MP Biomedicals, Illkirch, France).
An Illumina RNA amplification kit (Ambion, Austin, TX, USA) was used according to the manufacturer’s instructions to obtain biotinlabeled cRNA from 500 ng of total RNA.
Hybridizations to Illumina HumanWG-6 v3.0 Expression BeadChips (Illumina Inc., San Diego, CA, USA) containing probes for PLIN2 and PLIN5, were performed by the Finnish DNA Microarray Center at Turku Center for Biotechnology according to the Illumina BeadStation 500x manual.
Hybridized probes were detected with Cyanin-3-streptavidin (

1 μ g \cdot {mL}^{- 1}

, Amersham Biosciences, GE Healthcare, Uppsala, Sweden) using Illumina BeadArray Reader (Illumina Inc.) and BeadStudio v3 software (Illumina Inc.).
The gene expression data and the raw data sets for skeletal muscle have been deposited in the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20319, accessed on 5 January 2023).

Fachada V., Silvennoinen M., Sahinaho U.M., Rahkila P., Kivelä R., Hulmi J.J., Kujala U, & Kainulainen H. (2023). Effects of Long-Term Physical Activity and BCAA Availability on the Subcellular Associations between Intramyocellular Lipids, Perilipins and PGC-1α. International Journal of Molecular Sciences, 24(5), 4282.

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Multiomics Profiling of Cancer Cell Lines

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Gene expression data were obtained using Illumina Human WG-6 v3.0 Expression BeadChips (Illumina) and expression values log2 normalized. MicroRNA profiling was performed using a real-time PCR-based approach using miRCURY LNA Universal RT miRNA PCR (panel I+II) (Exiqon, Inc.). MicroRNA profiling was not available for cell lines H1299 and H1703. Illumina Infinium HumanMethylation27 BeadChips were used for DNA methylation analysis. DNA methylation profiling was not available for cell lines H1385 and H1703. mRNA, DNA methylation and microRNA datasets were deposited in the National Center for Biotechnology Information’s Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo).

Schliekelman M.J., Taguchi A., Zhu J., Dai X., Rodriguez J., Celiktas M., Zhang Q., Chin A., Wong C.H., Wang H., McFerrin L., Selamat S.A., Yang C., Kroh E.M., Garg K.S., Behrens C., Gazdar A.F., Laird-Offringa I.A., Tewari M., Wistuba I.I., Thiery J.P, & Hanash S.M. (2015). Molecular portraits of epithelial, mesenchymal and hybrid states in lung adenocarcinoma and their relevance to survival. Cancer research, 75(9), 1789-1800.

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RNA Extraction and Expression Analysis

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Total RNA was harvested from MDM using the RNeasy Mini Kit with RNase-free DNase treatment (Qiagen, Hilden, Germany), in accordance with the manufacturer's instructions. Optical density readings were determined for OD₂₆₀/OD₂₈₀ and OD₂₆₀/OD₂₃₀ using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Hemel Hempstead, UK) to assess protein and solvent contamination, respectively. RNA integrity was analysed by assessing ribosomal RNA band 28S/18S ratios using high-resolution electrophoresis on an Agilent Bioanalyser (Agilent Technologies, Inc, Berkshire, UK) and attained an integrity score of > 8. Total RNA (500 ng) was amplified using the Illumina TotalPrep-96 RNA Amplification kit (Life Technologies Ltd, Paisley, UK), normalized to 150 ng/μl, and 750 ng was hybridized to Illumina Human-WG6 v3.0 Expression BeadChips (Illumina, Essex, UK) for 16 hr at 58°. Bead arrays were stained with streptavidin-Cy3 (GE Healthcare, Amersham, UK) and scanned using the Bead array reader and processed with genomestudio® data analysis software (Illumina). Data were smoothed with cubic spline normalization.

Smith A.M., Sewell G.W., Levine A.P., Chew T.S., Dunne J., O'Shea N.R., Smith P.J., Harrison P.J., Macdonald C.M., Bloom S.L, & Segal A.W. (2014). Disruption of macrophage pro-inflammatory cytokine release in Crohn's disease is associated with reduced optineurin expression in a subset of patients. Immunology, 144(1), 45-55.

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Illumina Expression Profiling of Total RNA

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Total RNA was extracted from cell lines and tissues using the RNeasy Plus Mini Kit (Qiagen). RNA quality and concentration were checked using the Experion Automated Electrophoresis System (Bio-Rad) according to the manufacturer's protocol. Expression data were obtained using Illumina Human WG-6 v3.0 Expression BeadChips (Illumina) in the Genomics Core at The University of Texas Southwestern Medical Center at Dallas (Dallas, Texas). Bead-summarized data were obtained using Illumina BeadStudio software and pre-processed using the R software package MBCB (Model-based Background Correction for Beadarray) for background correction and probe summarization. Pre-processed data were quantile normalized and log transformed.

Taguchi A., Taylor A.D., Rodriguez J., Çeliktaş M., Liu H., Ma X., Zhang Q., Wong C.H., Chin A., Girard L., Behrens C., Lam W.L., Lam S., Minna J.D., Wistuba I.I., Gazdar A.F, & Hanash S.M. (2014). A search for novel cancer/testis antigens in lung cancer identifies VCX/Y genes expanding the repertoire of potential immunotherapeutic targets. Cancer research, 74(17), 4694-4705.

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Lung Adenocarcinoma Gene Expression Profiles

Cited 2 times

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Microarray data and the corresponding clinical data for non-smoking female patients with lung adenocarcinoma from the GSE32863 (14 (link)) and GSE75037 (15 (link)) datasets, both datasets of 24 non-smoking female patients, were downloaded from the Gene Expression Omnibus (GEO) (ncbi.nlm.nih.gov/geo/) based on the platform of GPL6884 Illumina Human WG-6 v3.0 expression beadchip (Illumina, Inc.). Data for 48 non-smoking female patients with lung adenocarcinoma detected using a microarray chip in the GEO database (GSE32863 and GSE75037) and from 160 non-smoking female patients with lung adenocarcinoma detected using RNA-sequencing in the The Cancer Genome Atlas (TCGA) database (portal.gdc.cancer.gov; last updated on July 2017) were also downloaded. The SVA package (version 3.32.1; www.bioconductor.org/help/search/index.html?q=sva/) in Bioconductor (version 3.9; www.bioconductor) was used to normalize the gene expression profile data.

Wang H., Zhang Z., Xu K., Wei S., Li L, & Wang L. (2019). Exploration of estrogen receptor-associated hub genes and potential molecular mechanisms in non-smoking females with lung adenocarcinoma using integrated bioinformatics analysis. Oncology Letters, 18(5), 4605-4612.

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Transcriptomic Profiling of Acute Myocardial Infarction

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In our research, we searched the datasets, which contained patients AMI and normal controls. The microarray expression datasets (GSE48060, GSE60993, GSE66360, GSE61144, GSE34198, and GSE97320) were downloaded from the GEO database¹ (11 (link)–13 (link)). The gene expression profiling dataset GSE48060 contained 49 AMIs and 50 controls collected from blood, while GSE66360 included 31 AMIs and 21 controls collected from circulating endothelial cells, which were both using the GPL570 platform of Affymetrix Human Genome U133 Plus 2.0 Array. In addition, the GSE60993 dataset included 7 AMIs and 7 controls collected from peripheral blood, which is based on the GPL6884 platform of Illumina HumanWG-6 v3.0 Expression BeadChip. In addition, the GSE61144 dataset was used as the validation set, which collects 7 AMIs and 10 control samples based on the GPL6106 platform of Sentrix Human-6 v2 Expression BeadChip, the dataset GSE34198 collects 49 AMIs and 48 controls based on GPL6102 platform of Illumina Human-6 v2.0 Expression BeadChip, and GSE97320 collects 3 AMIs and 3 controls using the GPL570 platform of Affymetrix Human Genome U133 Plus 2.0 Array.

Wu Y., Chen H., Li L., Zhang L., Dai K., Wen T., Peng J., Peng X., Zheng Z., Jiang T, & Xiong W. (2022). Construction of Novel Gene Signature-Based Predictive Model for the Diagnosis of Acute Myocardial Infarction by Combining Random Forest With Artificial Neural Network. Frontiers in Cardiovascular Medicine, 9, 876543.

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Gene Expression Profiling of Cancer Transcriptomes

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The datasets used in the present study were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) (8 (link)). The original gene expression profiles from the datasets GSE18842(9 (link)), GSE32863(10 (link)) and GSE29250(11 (link)) were used and the clinical information of the patients was obtained from the original research articles. The GSE18842 dataset included 91 samples (46 tumors and 45 controls) and all samples were paired except 2 tumors and 1 control. The platform used for the GSE18842 dataset was GPL570 (HG-U133_Plus_2) Affymetrix Human Genome U133 Plus 2.0 Array. The GSE32863 dataset included 116 samples (58 tumors and 58 controls) and all samples were paired. The platform used for the GSE32863 dataset was the GPL6884 Illumina Human WG-6 v.3.0 expression beadchip. The GSE29250 dataset included 12 samples (6 tumors and 6 controls) and all samples were paired. The platform used for the GSE29250 dataset was the GPL8179 Illumina Human v.2 MicroRNA expression beadchip.

Wang W., Wang S, & Pan L. (2020). Identification of key differentially expressed mRNAs and microRNAs in non-small cell lung cancer using bioinformatics analysis. Experimental and Therapeutic Medicine, 20(4), 3720-3732.

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Enchondroma Gene Expression Analysis

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In current study, the gene expression profiles of GSE22855 were downloaded from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/). GSE22855 was based on Illumina Inc GPL6884 platform (Illumina HumanWG-6 v3.0 expression beadchip). The GSE22855 dataset contained 13 samples, including 7 enchondromas samples and 6 control samples.

Shi Z., Zhou H., Pan B., Lu L., Kang Y., Liu L., Wei Z, & Feng S. (2017). Exploring the key genes and pathways in enchondromas using a gene expression microarray. Oncotarget, 8(27), 43967-43977.

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