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Mousewg 6 v2.0 expression beadchip

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The MouseWG-6 v2.0 Expression BeadChip is a gene expression profiling microarray platform designed for the analysis of mouse transcripts. The BeadChip provides a comprehensive coverage of the mouse genome, enabling researchers to measure the expression levels of thousands of genes simultaneously.

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Lab products found in correlation

Agilent 2100 bioanalyzer, by Agilent Technologies (5 mentions) Bioanalyzer, by Agilent Technologies (5 mentions) Rneasy mini kit, by Qiagen (5 mentions) Rneasy micro kit, by Qiagen (4 mentions) Trizol, by Thermo Fisher Scientific (4 mentions) Rnaeasy micro kit, by Qiagen (3 mentions) Humanht 12 v3 beadchip, by Illumina (2 mentions) Qubit rna hs assay kit, by Thermo Fisher Scientific (2 mentions) Mirvana kit, by Thermo Fisher Scientific (2 mentions) Rna 6000 nano kit, by Agilent Technologies (2 mentions) Omics explorer n n, by Qlucore (2 mentions) Genomestudio software, by Illumina (2 mentions) Genomestudio, by Illumina (2 mentions) Genespring gx11, by Agilent Technologies (2 mentions) Totalprep rna amplification kit, by Illumina (2 mentions) Ingenuity ipa software, by Qiagen (2 mentions) Genespring gx software, by Agilent Technologies (2 mentions) Totalprep 96 rna amplification kit, by Thermo Fisher Scientific (2 mentions) Agilent rna 6000 nano kit, by Agilent Technologies (2 mentions) Tri reagent, by Merck Group (2 mentions)

79 protocols using mousewg 6 v2.0 expression beadchip

1

Transcriptome Analysis of Adipose Tissue

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Epididymal white adipose tissue (eWAT) from the mice was analyzed with Illumina iScan and MouseWG-6 v2.0 Expression BeadChips (6 WT and 6 Irx5-KO mice), and the isolated human adipocytes were analyzed with the Illumina iScan and HumanHT-12 v.3 BeadChip. Raw data files were imported into J-Express. Before further analysis, missing values were replaced by the LSimpute_adaptive method [21 (link)] and signal intensity values were quantile normalized [22 (link)] and log transformed (base 2). The mouse and human datasets were combined based on ENSEMBL gene IDs. The genes identified in both datasets were then sorted based on similar or divergent expression in obesity. Ingenuity Pathway Analysis (IPA) was used to identify globally predominant gene networks (accessed on March 21, 2016).
Bjune J.I., Haugen C., Gudbrandsen O., Nordbø O.P., Nielsen H.J., Våge V., Njølstad P.R., Sagen J.V., Dankel S.N, & Mellgren G. (2018). IRX5 regulates adipocyte amyloid precursor protein and mitochondrial respiration in obesity. International journal of obesity (2005).
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2

Genome-wide Expression Profiling of Intestinal Samples

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RNA from mouse samples was obtained as described above, quantified spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with no evidence for RNA degradation (RNA integrity number >8) were kept for further experiments. Genome-wide gene expression profiling of the epithelium and LP of five individual DQ8, DQ8-Dd-villin-IL-15tg, and Dd-villin-IL-15tg mice were determined by using the MouseWG-6 v2.0 Expression BeadChips from Illumina. Low-level microarray analyses were performed in R, using the Bioconductor software package lumi29 . We first applied a variance stabilizing transformation to all arrays30 and then quantile normalized the data. After normalization, we removed probes with intensities indistinguishable from background noise (as measured by the negative controls present on each array).
Abadie V., Kim S.M., Lejeune T., Palanski B.A., Ernest J.D., Tastet O., Voisine J., Discepolo V., Marietta E.V., Hawash M.B., Ciszewski C., Bouziat R., Panigrahi K., Horwath I., Zurenski M.A., Lawrence I., Dumaine A., Yotova V., Grenier J.C., Murray J.A., Khosla C., Barreiro L.B, & Jabri B. (2020). IL-15, gluten and HLA-DQ8 drive tissue destruction in coeliac disease. Nature, 578(7796), 600-604.
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3

Schwann Cell Transcriptional Profiling

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MAL-overexpressing and wild-type Schwann cells were cultured and stimulated with 20 µM forskolin for 24 h (Schmid et al., 2014 ). Nine experimental samples were investigated per condition, derived from five independent experiments. Total RNA was isolated using RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol. All RNA samples had an RNA integrity number (RIN) of above 8, verified with the Agilent Bioanalyzer system (Agilent Technologies). RNA amplification, biotinylation, in vitro transcription, and cRNA hybridization were performed as described earlier (Kinter et al., 2013 (link); Schmid et al., 2014 ). MouseWG-6 v2.0 Expression BeadChips from Illumina were scanned using the iScan Reader (Illumina), and global median normalization of gene expression was performed with the GenomeStudio software (version 2011.1, Illumina). All data passed the quality control analysis as assessed by the Illumina on-board software (GenomeStudio, version 2011.1) and principal component analysis (PCA; Partek Genomics Suite, version 6.6, Partek Inc.). Significantly differentially expressed genes were further analyzed with the Ingenuity Pathway Analysis (IPA) software (Ingenuity Systems) and the Database for Annotation, Visualization and Integrated Discovery (DAVID, version 6.7, DAVID Bioinformatics Resources; Huang da, Sherman, & Lempicki, 2009 ).
Schmid D., Zeis T., Sobrio M, & Schaeren-Wiemers N. (2014). MAL Overexpression Leads to Disturbed Expression of Genes That Influence Cytoskeletal Organization and Differentiation of Schwann Cells. ASN NEURO, 6(5), 1759091414548916.
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4

Microarray and microRNA Profiling of Hindlimb Ischemia

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For microarray analysis, total RNA was isolated from adductor muscles using the RNeasy Fibrous Tissue Minikit (QIAGEN). RNA concentration, purity, and integrity were analyzed by nanodrop (nanodrop Technologies) and bioanalyzer (Agilent 2000) measurements.
For microRNA expression profiling, adductor muscle tissue from days 0, 1, 3, and 7 after induction of hindlimb ischemia was used. MicroRNA expression profiling was performed as described previously using locked nucleic acid (LNA)-based arrays (miRCURY LNA miR Array Ready-to-Spot Probe Set, Exiqon).27 (link) Normalization and background correction were performed in the “statistical language R” using the “vsn” package (Bioconductor). Differential expression was assayed using the “limma” package (Bioconductor) by fitting the eBayes linear model and contrasting individual treatments with untreated controls. Log2 fold changes were calculated using the toptable function of the limma package.4 (link), 45 (link)
For whole-genome expression profiling, adductor muscle tissue from days 0, 1, 3, 7, 14, and 28 after induction of hindlimb ischemia was used. Whole-genome expression profiling was performed using MouseWG-6 v2.0 Expression Beadchips (Illumina), and expression levels were Log2-transformed as described previously.27 (link), 43 (link)
Downie Ruiz Velasco A., Welten S.M., Goossens E.A., Quax P.H., Rappsilber J., Michlewski G, & Nossent A.Y. (2018). Posttranscriptional Regulation of 14q32 MicroRNAs by the CIRBP and HADHB during Vascular Regeneration after Ischemia. Molecular Therapy. Nucleic Acids, 14, 329-338.
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5

Microarray Analysis of Mouse Transcriptome

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Mouse microarrays were performed using Illumina® MouseWG-6 v2.0 Expression BeadChips (Illumina). Samples were labeled and hybridized using Illumina® TotalPrep™ kit (Ambion) and then arrays were scanned using Illumina® Beadstation 500 BeadArray reader and data acquisitioned with BeadStudio (Illumina®). R 2.15.1 (http://www.R-project.org/) and tools in Bioconductor (http://www.bioconductor.org/) were used for all analyses unless otherwise stated. More detailed methodology, including flowchart and Sweave report, for microarray and survival analyses in Supplementary Methods.
Delgado O., Batten K.G., Richardson J.A., Xie X.J., Gazdar A.F., Kaisani A.A., Girard L., Behrens C., Suraokar M., Fasciani G., Wright W.E., Story M.D., Wistuba I.I., Minna J.D, & Shay J.W. (2014). Radiation-enhanced Lung Cancer Progression in a Transgenic Mouse Model of Lung Cancer is Predictive of Outcomes in Human Lung and Breast Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research, 20(6), 1610-1622.
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6

Microarray Analysis of Mouse Gene Expression

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Mouse WG-6 v2.0 Expression BeadChips (Illumina) were used for microarray hybridizations. Total RNA was prepared using the NucleoSpin RNA II kit. RNA quality was confirmed via Nanodrop-1000 spectrometric analysis and via a Bioanalyzer (Agilent Technologies). 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit with oligo(dT) priming (Ambion). 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16–20 hours. After hybridization, the array was washed with buffer at 55°C and blocked at room temperature. Bound, biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Dried arrays were scanned with the iScan System, and data with quantile normalization was exported from GenomeStudio v2011.1 Gene Expression Module 1.9.0 and imported to GeneSpring. Differentially expressed genes with >1.5-fold change were subjected to pathway analysis using Ingenuity Systems software. Analysis of fold-change between paired samples was conducted without subtraction of background signal. Primary microarray data is available from GEO (accession number GSE55760).
Ma O., Hong S., Guo H., Ghiaur G, & Friedman A.D. (2014). Granulopoiesis Requires Increased C/EBPα Compared to Monopoiesis, Correlated with Elevated Cebpa in Immature G-CSF Receptor versus M-CSF Receptor Expressing Cells. PLoS ONE, 9(4), e95784.
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7

Transcriptome Analysis of Mouse Samples

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RNA samples were assessed by Agilent for integrity, purity, and concentration. Samples passing quality control were analyzed on Illumina mouse WG-6 v 2.0 expression BeadChips in the Mayo Clinic Medical Genome Facility Gene Expression Core. Expression data were analyzed using Excel and MatLab [7 (link)]. Heatmaps and hierarchical clusters were derived using Gitools v2.2.2 and pathway identification was performed using Ingenuity Pathway Analysis.
Walker-Caulfield M.E., Guo Y., Johnson R.K., McCarthy C.B., Fitz-Gibbon P.D., Lucchinetti C.F, & Howe C.L. (2015). NFκB signaling drives pro-granulocytic astroglial responses to neuromyelitis optica patient IgG. Journal of Neuroinflammation, 12, 185.
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8

Genome-wide Expression Profiling of Intestinal Samples

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RNA from mouse samples was obtained as described above, quantified spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with no evidence for RNA degradation (RNA integrity number >8) were kept for further experiments. Genome-wide gene expression profiling of the epithelium and LP of five individual DQ8, DQ8-Dd-villin-IL-15tg, and Dd-villin-IL-15tg mice were determined by using the MouseWG-6 v2.0 Expression BeadChips from Illumina. Low-level microarray analyses were performed in R, using the Bioconductor software package lumi29 . We first applied a variance stabilizing transformation to all arrays30 and then quantile normalized the data. After normalization, we removed probes with intensities indistinguishable from background noise (as measured by the negative controls present on each array).
Abadie V., Kim S.M., Lejeune T., Palanski B.A., Ernest J.D., Tastet O., Voisine J., Discepolo V., Marietta E.V., Hawash M.B., Ciszewski C., Bouziat R., Panigrahi K., Horwath I., Zurenski M.A., Lawrence I., Dumaine A., Yotova V., Grenier J.C., Murray J.A., Khosla C., Barreiro L.B, & Jabri B. (2020). IL-15, gluten and HLA-DQ8 drive tissue destruction in coeliac disease. Nature, 578(7796), 600-604.
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9

Transcriptomic Analysis of Gene Expression

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Total RNA was extracted with QIAGEN RNeasy kits for analysis of gene expression by Illumina Mouse WG-6 v2.0 Expression BeadChips or by TaqMan Assays. RT of RNA for qRT-PCR was performed using Multiscribe DNA polymerase (Applied Biosystems), and PCR was performed in 10-µl reactions on a 7500 Real-Time PCR System (Applied Biosystems). All procedures were conducted according to the manufacturer’s instructions. Illumina data were checked for quality, background corrected, and quantile normalized with GenomeStudio (Illumina). Analysis of differential expression was conducted with GenomeStudio for probe sets filtered by spot detection (P < 0.01) and difference in mean signal intensity between treatment groups (dif > 20). Significantly changed genes were subjected to analysis of canonical pathways curated by Ingenuity (IPA, Ingenuity Systems). Gene set expression analysis (GSEA) was conducted with unfiltered genes using curated gene lists downloaded from MSigDB. Ranked gene list data were imported into Cytoscape for visualization of functional enrichments with Enrichment Map using edge-weighted force-directed layout. Heat maps were generated using genes selected from differential gene expression analysis in GenePattern. Expression data have been deposited for public access in the NCBI Gene Expression Omnibus (GEO) under accession no. GSE62463.
Diaz M.F., Li N., Lee H.J., Adamo L., Evans S.M., Willey H.E., Arora N., Torisawa Y.S., Vickers D.A., Morris S.A., Naveiras O., Murthy S.K., Ingber D.E., Daley G.Q., García-Cardeña G, & Wenzel P.L. (2015). Biomechanical forces promote blood development through prostaglandin E2 and the cAMP–PKA signaling axis. The Journal of Experimental Medicine, 212(5), 665-680.
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10

Transcriptome Analysis of Adipose Tissue

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Epididymal white adipose tissue (eWAT) from the mice was analyzed with Illumina iScan and MouseWG-6 v2.0 Expression BeadChips (6 WT and 6 Irx5-KO mice), and the isolated human adipocytes were analyzed with the Illumina iScan and HumanHT-12 v.3 BeadChip. Raw data files were imported into J-Express. Before further analysis, missing values were replaced by the LSimpute_adaptive method [21 (link)] and signal intensity values were quantile normalized [22 (link)] and log transformed (base 2). The mouse and human datasets were combined based on ENSEMBL gene IDs. The genes identified in both datasets were then sorted based on similar or divergent expression in obesity. Ingenuity Pathway Analysis (IPA) was used to identify globally predominant gene networks (accessed on March 21, 2016).
Bjune J.I., Haugen C., Gudbrandsen O., Nordbø O.P., Nielsen H.J., Våge V., Njølstad P.R., Sagen J.V., Dankel S.N, & Mellgren G. (2018). IRX5 regulates adipocyte amyloid precursor protein and mitochondrial respiration in obesity. International journal of obesity (2005).
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