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Iscan bead array scanner

Manufactured by Illumina
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The iScan Bead Array Scanner is a high-throughput, multi-sample microarray scanning system designed for use with Illumina's BeadChip arrays. The iScan system captures high-resolution image data from the BeadChip samples, which can then be processed and analyzed using Illumina's software and bioinformatics tools.

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Lab products found in correlation

Genomestudio, by Illumina (2 mentions) Bioanalyzer 6000, by Agilent Technologies (1 mentions) Ez dna methylation kit, by Zymo Research (1 mentions) Omics explorer, by Qlucore (1 mentions) Humanmethylation450 beadchip, by Illumina (1 mentions) Infinium humanmethylation450 beadchip, by Illumina (1 mentions) Picogreen reagent, by Thermo Fisher Scientific (1 mentions) Bisulfite conversion kit, by Zymo Research (1 mentions) Dneasy kit, by Qiagen (1 mentions) Mouseref 8 v2.0 beadchips, by Illumina (1 mentions) Iscan control software, by Illumina (1 mentions) Experion, by Bio-Rad (1 mentions) Genomestudio software, by Illumina (1 mentions) Mouseref 8 v2.0 expression beadchip, by Illumina (1 mentions) Totalprep rna amplification kit, by Thermo Fisher Scientific (1 mentions)

5 protocols using iscan bead array scanner

1

DNA Methylation Analysis Workflow

Cited 1 time
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DNA quality was checked using the BioAnalyzer 6000 (Agilent) according to the manufacturer's protocol. DNA was bisulfite converted using the EZ DNA methylation kit (Zymo Research) according to the manufacturer's protocol. Bisulfite converted DNA was processed and hybridized to HumanMethylation450 BeadChips (Illumina), which were scanned with an Illumina iScan Bead Array Scanner per the manufacturer's protocol. DNA methylation data IDAT files for each samples were used for processing and SWAN normalization and differential analysis on M values using the minfi Bioconductor package in R [18 (link)]. A total of 48 samples were used for analysis. principal component analysis (PCA), hierarchical clustering, was performed using Qlucore Omics Explorer (version 2.3).
Wolfe L.M., Thiagarajan R.D., Boscolo F., Taché V., Coleman R.L., Kim J., Kwan W.K., Loring J.F., Parast M, & Laurent L.C. (2014). Banking placental tissue: An optimized collection procedure for genome-wide analysis of nucleic acids. Placenta, 35(8), 645-654.
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2

Genome-Wide DNA Methylation Analysis

Cited 2 times
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DNA was extracted from 106 cells (Qiagen DNeasy kit) according to the manufacturer’s protocol and quantified using the Picogreen reagent (Life Technologies). Bisulfite conversion was performed using the Bisulfite Conversion Kit from Zymo Research. Bisulfite converted DNA was labeled and hybridized to Infinium HumanMethylation450 BeadChips (Illumina, Inc.), scanned with an Illumina iScan BeadArray Scanner and quality controlled in GenomeStudio (Illumina, Inc.). Pathway analysis was performed using GREAT [17 (link)], and visualized using REVIGO [18 (link)].
Garitaonandia I., Amir H., Boscolo F.S., Wambua G.K., Schultheisz H.L., Sabatini K., Morey R., Waltz S., Wang Y.C., Tran H., Leonardo T.R., Nazor K., Slavin I., Lynch C., Li Y., Coleman R., Gallego Romero I., Altun G., Reynolds D., Dalton S., Parast M., Loring J.F, & Laurent L.C. (2015). Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions. PLoS ONE, 10(2), e0118307.
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3

Illumina-based Transcriptome Analysis of Mouse Samples

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Prior to gene expression experiments, total RNA integrity was confirmed using the Experion™ automated gel electrophoresis system (BioRad, Munich, Germany). cRNA sample preparation for hybridisation on the Illumina gene expression platform was performed using the TargetAmp™ Nano-g™ Biotin-aRNA Kit for the Illumina System (Epicentre/Biozym, Hess. Oldendorf, Germany) starting with 250 ng of total RNA. Samples were hybridized according to manufacturer's instructions on Mouse Ref-8 v2.0 Bead Chips (Illumina, San Diego, USA). Each chip comprises probes of 25,700 coding and non-coding RNA transcripts. Read outs of hybridisation signal intensities were performed on an iScan Bead Array scanner (Illumina, San Diego, USA), data pre-processing including spot detection, gene mapping and averaging of replicates was performed with iScan Control Software and GenomeStudio software (Illumina, San Diego). The data are accessible through Gene Expression Omnibus series [GSE67241].
Manchanda H., Seidel N., Blaess M.F., Claus R.A., Linde J., Slevogt H., Sauerbrei A., Guthke R, & Schmidtke M. (2016). Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus. Frontiers in Microbiology, 7, 1167.
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4

Genotyping iPSC Clones with SNP Arrays

Cited 1 time
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Genomic DNA from iPSC clones modified by gene editing were genotyped using an Infinium OmniExpress-24 v1.2 and v1.3 (Illumina) SNP array according to the manufacturer’s recommendations. Median probe spacing is around 2 kb. Array scanning was performed on an iScan Bead Array Scanner (Illumina). Scanned data were processed using Illumina GenomeStudio (2011.1 for v1.2 and 2.0.4 for v1.3) with human genome Build 37 and FinalReports were exported according to the manufacturer’s protocol. CNV call was done using a combination of PennCNV53 (link) (1.0.3), GWASTools54 (link) (v1.2.R), and MAD55 (link) (1.0.1). Karyograms were prepared using GenomeJack (Mitsubishi Space Software).
Grajcarek J., Monlong J., Nishinaka-Arai Y., Nakamura M., Nagai M., Matsuo S., Lougheed D., Sakurai H., Saito M.K., Bourque G, & Woltjen K. (2019). Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations. Nature Communications, 10, 4856.
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5

Microarray Analysis of MYF5 RIP Samples

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RNA present in the MYF5 RIP samples was isolated using TRIzol extraction and amplified and labeled using the Illumina TotalPrep RNA Amplification Kit following the manufacturer's protocol (Thermo-Fisher, Waltham, MA). Biotinylated RNA hybridized to MouseRef-8 v2.0 Expression BeadChips (Illumina, San Diego, CA) was visualized using streptavidin-conjugated Cy3 staining and scanned at 0.53-μm resolution on an Illumina iScan Beadarray scanner. Raw microarray data were filtered by detection P-values of <0.02, normalized by Z-score transformation and tested for significant differences in signal intensity by Z-test and multiple comparison correction by false discovery rate, with additional sample group ANOVA test to control overall sample error. The sample quality was analyzed by scatter plot, principal component analysis and gene sample Z-score-based hierarchy clustering to exclude possible outliers. Transcripts were considered to be significantly changed when they had Z-test P-values of ≤0.05, Z-ratio absolute values of Z-ratio ≥1.5, a multiple-comparison correction false-discovery rate of ≤0.30, non-negative average Z-score signal of the comparison group samples, and an independent one-way analysis of variance (ANOVA) on sample group analysis P-value of ≤0.05.
Panda A.C., Abdelmohsen K., Martindale J.L., Di Germanio C., Yang X., Grammatikakis I., Noh J.H., Zhang Y., Lehrmann E., Dudekula D.B., De S., Becker K.G., White E.J., Wilson G.M., de Cabo R, & Gorospe M. (2016). Novel RNA-binding activity of MYF5 enhances Ccnd1/Cyclin D1 mRNA translation during myogenesis. Nucleic Acids Research, 44(5), 2393-2408.
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