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Hiscan

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The HiScan is a high-performance microarray scanner designed for use with Illumina's DNA analysis platforms. It provides reliable and accurate scanning of microarray slides, generating high-quality image data for downstream analysis.

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Lab products found in correlation

Genomestudio, by Illumina (10 mentions) Genomestudio software, by Illumina (10 mentions) Infinium humanmethylation450 beadchip, by Illumina (6 mentions) Ez dna methylation kit, by Zymo Research (5 mentions) Hiseq 2000, by Illumina (4 mentions) Whole genome gene expression direct hybridization assay, by Illumina (3 mentions) Ambion tempus rna spin kit, by Thermo Fisher Scientific (3 mentions) Agilent 2100 bioanalyzer rna nano assay, by Agilent Technologies (3 mentions) Totalprep 96 rna amplification kit for array analysis, by Illumina (3 mentions) Human ht 12 expression beadchips, by Illumina (3 mentions) Humanht 12 v4 expression beadchip, by Illumina (3 mentions) Totalprep rna amplification kit, by Illumina (3 mentions) Infinium methylationepic beadchip assay epic array, by Illumina (3 mentions) Bioanalyzer, by Agilent Technologies (3 mentions) Allprep dna rna protein kit, by Qiagen (3 mentions) Rneasy mini kit, by Qiagen (3 mentions) Ht 12 v4 expression beadchip, by Illumina (3 mentions) Dnase, by Thermo Fisher Scientific (3 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Zymo ez dna methylation kit, by Zymo Research (2 mentions)

82 protocols using hiscan

1

Genome-wide DNA Methylation Profiling

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Five hundred nanograms of DNA samples from each study subject was used for genome-wide DNA methylation sequencing analysis. Samples were prepared using the Illumina Infinium Human MethylationEPIC BeadChip platform following the manufacturer's standard protocol. Subsequently, the prepared samples were scanned with Illumina HiScan (Illumina, Inc.), and DNA methylation levels were analyzed using GenomeStudio software v2011.1. The analysis covered more than 850,000 CpG sites.
Chen C.S., Yuan T.H., Lu T.P., Lee H.Y., Chen Y.H., Lai L.C., Tsai M.H., Chuang E.Y, & Chan C.C. (2024). Exposure-associated DNA methylation among people exposed to multiple industrial pollutants. Clinical epigenetics, 16(1).
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2

Genome-Wide DNA Methylation Profiling

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Blood samples were collected from all participants. Purified DNA was quantified on a Qubit Fluorometer (Thermo Fisher Scientific, United States) and for each sample 500 ng was bisulphite-converted using EZ DNA Methylation Kits (Zymo Research, United States). The samples were then assayed for genome-wide DNA methylation levels using Illumina EPIC DNA methylation arrays that offer a high coverage of CpGs >850,000 CpG sites at single-nucleotide resolution, covering all known genes (96% Refseq genes). All procedures were performed according to the manufacturer’s protocol, and arrays were scanned on an Illumina HiScan (Illumina, United States) at the Genomics Research Centre, QUT.
Bainomugisa C.K., Sutherland H.G., Parker R., Mcrae A.F., Haupt L.M., Griffiths L.R., Heath A., Nelson E.C., Wright M.J., Hickie I.B., Martin N.G., Nyholt D.R, & Mehta D. (2021). Using Monozygotic Twins to Dissect Common Genes in Posttraumatic Stress Disorder and Migraine. Frontiers in Neuroscience, 15, 678350.
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3

Infinium® II SNP Array Genotyping

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The apple and pear Infinium® II 9 K SNP array [47 , 48 ] was used for SNP genotyping following the Infinium® HD Assay Ultra protocol, and scanned with the Illumina HiScan (Illumina Inc., San Diego, USA).
Data were analysed using Illumina’s GenomeStudio v 1.0 software Genotyping Module, setting a GenCall threshold of 0.15. The software automatically determines the cluster positions of the AA/AB/BB genotypes for each SNP and displays them in normalized graphs. SNPs were filtered for GenTrain score > 0.60 and 87% missing calls; additionally SNPs exhibiting the presence of null allele in the progeny or the parents were removed. The SNP 9 K array data were analysed by chromosome using the GenAlEx Software [43 (link)] to assess genetic relationships among progeny and parents.
Pasqualetto G., Palmieri L., Martens S., Bus V.G., Chagné D., Wiedow C., Malnoy M.A, & Gardiner S.E. (2022). Molecular characterization of intergeneric hybrids between Malus and Pyrus. Horticulture Research, 10(1), uhac239.
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4

Genome-wide DNA methylation profiling

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DNA was extracted from buccal swabs using the Isohelix DNA isolation kit (Cell Projects, Kent, UK). Seven hundred and fifty nanograms of genomic DNA was subjected to bisulfite conversion using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA, USA), which converts DNA methylation information into sequence base differences by deaminating unmethylated cytosines to uracil while leaving methylated cytosines unchanged. One hundred and sixty nanograms of converted DNA was applied to the HumanMethylation450 BeadChip array from Illumina (450K array), which enables the simultaneous quantitative measurements of 485,512 CpG sites across the human genome, following the manufacturer’s instructions. Chips were scanned on an Illumina HiScan, with the 214 samples run in two batches and each containing an equal number of FASD and control samples, randomly distributed across the chips. Two pairs of technical replicates were included and showed a Pearson correlation coefficient r > 0.996 in both cases, highlighting the technology’s reproducibility.
Portales-Casamar E., Lussier A.A., Jones M.J., MacIsaac J.L., Edgar R.D., Mah S.M., Barhdadi A., Provost S., Lemieux-Perreault L.P., Cynader M.S., Chudley A.E., Dubé M.P., Reynolds J.N., Pavlidis P, & Kobor M.S. (2016). DNA methylation signature of human fetal alcohol spectrum disorder. Epigenetics & Chromatin, 9, 25.
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5

Genome-Wide DNA Methylation Profiling

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DNA was isolated from samples obtained at two time points (pre- and post-treatment). Bisulfite conversion was performed using 500 ng of DNA with EZ DNA Methylation-Direct Kit (Zymo, Irvine, CA, USA). The next steps were performed according to the Illumina protocol of Methylation EPIC kit (Illumina, San Diego, CA, USA). Bisulfite-converted-DNA was amplified (whole-genome amplification), fragmented, and precipitated. After resuspension, DNA was hybridized onto Bead Chips for 24 h at 37°C. The non-hybridized and nonspecifically hybridized DNA was washed away following extension and staining. Imaging was performed using HiScan (Illumina, USA).
Ludwig-Slomczynska A.H., Borys S., Seweryn M.T., Hohendorff J., Kapusta P., Kiec-Wilk B., Pitera E., Wolkow P.P, & Malecki M.T. (2019). DNA methylation analysis of negative pressure therapy effect in diabetic foot ulcers. Endocrine Connections, 8(11), 1474-1482.
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6

Whole Exome Sequencing and Variant Analysis

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We extracted DNA from whole blood and quantified it with a fluorometer (Qubit; Life Technologies Corporation, Carlsbad, CA, USA). The exome was captured and enriched from genomic DNA using an exome enrichment kit (Nextera; Illumina Inc., San Diego, CA, USA), representing 62 Mbp of the human genome (hg19 build). Sequencing was performed with a high-resolution optical imaging system (HiScan; Illumina Inc.).
Fragments were aligned to the hg19 reference genome through the use of Burrows-Wheeler alignment [41 (link)], and variant calling was performed with a software package for the analysis of sequence data (Genome Analysis Toolkit; Broad Institute, Cambridge, MA, USA) [42 (link)–44 ]. A total of 800 informative single nucleotide polymorphisms were analyzed with the whole-genome association analysis toolset (PLINK; http://pngu.mgh.harvard.edu/~purcell/plink/) to confirm the familial relationship between samples [45 (link)]. For genotype calls (in all members of the quartet, we used only reads with a Phred score ≥ 30 [46 (link)], bases with ≥ 20 reads, and a genotype quality score ≥ 20 [33 (link)].
Reis V.N., Kitajima J.P., Tahira A.C., Feio-dos-Santos A.C., Fock R.A., Lisboa B.C., Simões S.N., Krepischi A.C., Rosenberg C., Lourenço N.C., Passos-Bueno M.R, & Brentani H. (2017). Integrative Variation Analysis Reveals that a Complex Genotype May Specify Phenotype in Siblings with Syndromic Autism Spectrum Disorder. PLoS ONE, 12(1), e0170386.
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7

Illumina Whole Genome-DASL Expression Analysis

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The Illumina Whole Genome-DASL assay was performed using 200 ng of RNA following the manufacturer's instructions. Briefly, RNA was reverse transcribed to cDNA using biotinylated primers, followed by immobilization to streptavidin-conjugated paramagnetic particles. Biotinylated cDNAs were then simultaneously annealed to a set of assay-specific oligonucleotides. Extension and ligation of the annealed oligonucleotides generated PCR templates that were amplified using Titanium Taq DNA Polymerase (Clontech). Labeled PCR products were washed and denatured to yield single-stranded fluorescent molecules, which were hybridized to the HumanHT12 v4.0 Whole Genome Gene Expression BeadChips for 16 h at 58°C. The Illumina HiScan was used to scan the arrays.
Borys A.M., Seweryn M., Gołąbek T., Bełch Ł., Klimkowska A., Totoń-Żurańska J., Machlowska J., Chłosta P., Okoń K, & Wołkow P.P. (2019). Patterns of gene expression characterize T1 and T3 clear cell renal cell carcinoma subtypes. PLoS ONE, 14(5), e0216793.
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8

Transcriptome Profiling of Tumor Samples

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Tissues were snap frozen in TRIzol (Invitrogen) and stored at −80 C until use. RNA was prepared and treated with DNAse (Thermo Scientific). 4-6 distinct tumors were used per group covering 2-3 independent experiments. RNA quality was checked using an Agilent Bioanalyzer (Santa Clara, CA) and biotin-labeled using an Illumina TotalPrep-96 RNA Amplification Kit (Illumina). RNA expression detection was performed using the Illumina Mouse Ref-8 v2 BeadChip (Illumina, San Diego, CA). Microarrays were scanned using an Illumina HiScan. Raw signal intensities of each probe were obtained using data analysis software (Genome Studio; Illumina) and imported into Partek after quantile normalization and background subtraction. Differentially expressed genes were identified using Analysis of Variance (ANOVA) model. We filtered differentially expressed genes with ≥ ± 2.0-fold change and an FDR <0.05. Gene specific expression analysis were performed using the GSEA package (22 (link)). Pathway analysis on differentially expressed genes and CIS were assessed using Ingenuity IPA. Microarray data have been deposited in Gene Expression Omnibus (Accession numbers GSE59950 and GSE59951).
Zhong R., Bao R., Faber P.W., Bindokas V.P., Bechill J., Lingen M.W, & Spiotto M.T. (2015). Notch1 activation or loss promotes HPV-induced oral tumorigenesis. Cancer research, 75(18), 3958-3969.
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9

Genome-wide Expression Profiling using Illumina HT12v4

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Genome-wide gene expression profiles were generated using Illumina’s Infinium HT12v4 BeadChip assay (Illumina). The assay allows the determination of gene expression of > 47.000 probes covering designable RefSeq genes. The Infinium Expression Assay was performed according to the manufacturer’s instructions. The scanning was performed using an Illumina HiScan. Data from these images were loaded into Illumina’s GenomeStudio software suite (GS) and exported as a GS export file.
de Boni L., Gasparoni G., Haubenreich C., Tierling S., Schmitt I., Peitz M., Koch P., Walter J., Wüllner U, & Brüstle O. (2018). DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling. Clinical Epigenetics, 10, 13.
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10

Brassica Genotyping via Infinium Array

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The cluster file for B. napus was generated at AAFC through analysis of 437 genotypes and at TraitGenetics through the analysis of 432 genotypes. The cluster files for B. oleracea and B. rapa were generated with 129 and 121 samples, respectively. In both laboratories, DNA was extracted from young leaf tissue of greenhouse grown plants using a cetyltrimethylammonium bromide (CTAB)-based method (Murray and Thompson 1980 (link)). DNA was quantified and 200 ng were hybridised to the Brassica 60 K Infinium array as described in the manufacturer’s protocol (Illumina Inc., San Diego, CA). The arrays were scanned using an Illumina HiScan or BeadArray Reader, and SNP data were analysed using the Genotyping module of the GenomeStudio software package with the setting for the No Call threshold set to 0.05.
Clarke W.E., Higgins E.E., Plieske J., Wieseke R., Sidebottom C., Khedikar Y., Batley J., Edwards D., Meng J., Li R., Lawley C.T., Pauquet J., Laga B., Cheung W., Iniguez-Luy F., Dyrszka E., Rae S., Stich B., Snowdon R.J., Sharpe A.G., Ganal M.W, & Parkin I.A. (2016). A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 129(10), 1887-1899.
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