Iscan platform

Manufactured by Illumina

Sourced in United States, United Kingdom

The iScan platform is a high-throughput microarray scanning system designed for genetic analysis and molecular research. It provides accurate and efficient data acquisition for a range of microarray applications. The iScan system is capable of scanning multiple microarray types and supports a variety of sample formats.

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Infinium iScan platform (2 citations)

30 protocols using iscan platform

Genotyping Porcine Samples Using Illumina SNP60K

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DNA was extracted from porcine blood leukocytes using the conventional phenol-chloroform protocol [40 (link)]. DNA concentration and quality were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). All genomic DNA samples were normalized to 50 ng/μL in a 96-well plate. Samples were genotyped with the Illumina’s Porcine SNP60K v2 BeadChip (Illumina, San Diego, CA) using the iScan platform (Illumina, San Diego, CA, USA) according to manufacturer’s instructions. Clustering and genotype calling were performed using the genotyping module implemented in the Genome Studio software (Illumina, San Diego, CA, USA). The mapping data was derived from Pig60K_SNP_pos_build10.2.txt.gz with 62,633 SNPs (last modified by Groenen et al. on 7 July 2014; http://www.animalgenome.org/repository/pig/).

Wang L., Mu Y., Xu L., Li K., Han J., Wu T., Liu L., Gao Q., Xia Y., Hou G., Yang S., He X., Liu G.E, & Feng S. (2019). Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs. Animals : an Open Access Journal from MDPI, 9(6), 314.

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Genome-wide Gene Expression Analysis of C. albicans in Sepsis

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Genome-wide gene expression of C. albicans was analysed with C. albicans-specific microarrays (ClinEuroDiag). The red channel represents hybridization with Cy5-labeled C. albicans RNA from experimental mouse sepsis while the green channel always shows hybridization with Cy3-labeled RNA from C. albicans yeast cells growing logarithmically in standard YPD medium at 37 °C with shaking (common control). C. albicans RNA labelling, microarray hybridization, and scanning were performed as previously described24 (link).
Genome-wide gene expression profiling of mouse samples was performed using the MouseRef-8 (link) Expression and MouseWG6 v2.0 BeadChips (Illumina) according to the manufacturer’s instruction. From the RNA isolation, 200 ng total RNA with a Bioanalyzer RIN greater than seven were used for amplification prior to chip hybridization. Samples were analysed using the iScan platform (Illumina) measuring the variation of expression rate of > 42,000 transcripts. All microarray data are MIAME compliant and raw data have been deposited at GEO (GSE83682). The gene expression of liver, spleen, and kidney tissue 8 h, 12 h, 24 h, and 72 h after intravenous infection was compared to control samples of mock infected mice 24 h after PBS injection.

Hebecker B., Vlaic S., Conrad T., Bauer M., Brunke S., Kapitan M., Linde J., Hube B, & Jacobsen I.D. (2016). Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions. Scientific Reports, 6, 36055.

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Genome-wide Homozygosity Mapping

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To investigate the possible involvement of chromosomal aberrations and for the purpose of homozygosity mapping, HumanCytoSNP-12 v2.1 microarray containing 200 000 single nucleotide polymorphisms (SNPs) throughout the genome was used together with iScan platform (Illumina) to analyse all 10 available samples described. The common region of homozygosity among the affected individuals was mapped using GenomeStudio data analysis software (Illumina).

Jelani M., Dooley H.C., Gubas A., Mohamoud H.S., Khan M.T., Ali Z., Kang C., Rahim F., Jan A., Vadgama N., Khan M.I., Al-Aama J.Y., Khan A., Tooze S.A, & Nasir J. (2019). A mutation in the major autophagy gene, WIPI2, associated with global developmental abnormalities. Brain, 142(5), 1242-1254.

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EPIC Array-Based Genome-Wide DNA Methylation Profiling

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DNA was extracted from whole blood following the MasterPure™ DNA Purification kit (Epicentre, MCD 85201). DNA passing quality control based on NanoDrop spectrometry and in sufficient amount through the Qubit dsDNA Broad Range Assay Kit (ThermoFischer Scientific, Q32850) was selected for analysis for genome-wide DNAm status. 500 ng of genomic DNA from each sample was bisulfite-converted with the EZ DNA Methylation™ Kit (Zymo Research, D5002) and analyzed using Infinium HumanMethylationEPICBeadChip™ Kit (Illumina, WG-317-1002). The Illumina iScan platform scanned the arrays.

Marra P.S., Yamanashi T., Crutchley K.J., Wahba N.E., Anderson Z.E., Modukuri M., Chang G., Tran T., Iwata M., Cho H.R, & Shinozaki G. (2023). Metformin use history and genome-wide DNA methylation profile: potential molecular mechanism for aging and longevity. Aging (Albany NY), 15(3), 601-616.

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Genome-Wide Genotyping via Infinium GSA

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DNA isolation from the collected biomaterial and data generation were performed using the Infinium Global Screening Array (GSA) v3.0 run on the Illumina iScan Platform at TellmeGen CA (Valencia, Spain). A total of 650,000 genetic markers were analyzed using 10,000 probes (99.99% reliability). A triplicate analysis was performed.

Perfilyeva A., Bespalova K., Perfilyeva Y., Skvortsova L., Musralina L., Zhunussova G., Khussainova E., Iskakova U., Bekmanov B, & Djansugurova L. (2022). Integrative Functional Genomic Analysis in Multiplex Autism Families from Kazakhstan. Disease Markers, 2022, 1509994.

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Cytogenomic Analysis of Affected Individuals

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Genomic DNA of three affected (V-1, V-2, V-6) and one unaffected (V-3) individual was subjected to 300 K HumanCytoSNPs12 microarray analysis using an iScan platform (Illumina, USA) following the manufacturer’s protocols. The common regions of homozygosity were identified using GenomeStudio Genotyping Module v1.0 (Illumina).

Alkhiary Y.M., Jelani M., Almramhi M.M., Mohamoud H.S., Al-Rehaili R., Al-Zahrani H.S., Serafi R., Yang H, & Al-Aama J.Y. (2015). Whole-exome sequencing reveals a recurrent mutation in the cathepsin C gene that causes Papillon–Lefevre syndrome in a Saudi family. Saudi Journal of Biological Sciences, 23(5), 571-576.

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Illumina Omni5 Exome Genotyping Protocol

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The samples were genotyped on the Illumina Omni5 Exome Bead Chip v.4.0.1 (Illumina Inc., San Diego, CA, United States) which contains 4.6 million single nucleotide polymorphism (SNP). Illumina recommended the standard protocol was used for sample hybridization and scanning using the Illumina iScan platform.

Tay G.K., Henschel A., Daw Elbait G, & Al Safar H.S. (2020). Genetic Diversity and Low Stratification of the Population of the United Arab Emirates. Frontiers in Genetics, 11, 608.

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Whole Genome Genotyping and Homozygosity Mapping

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Whole genome SNP genotyping array was performed using Illumina iScan platform and HumanOmni 2.5M bead chip, genotyping 2.5 million SNPs. Approximately 200 ng genomic DNA of two affected and two unaffected members were taken for genotyping as per protocol described elsewhere.
26 (link)
27 (link)
Illumina genome studio and homozygosity mapper
28 (link)
29 (link)
were employed to detect common regions sharing homozygosity amongst the affected members.

Almatrafi A., Hashmi J.A., Fadhli F., Alharbi A., Afzal S., Ramzan K, & Basit S. (2021). Further Evidence of a Recessive Variant in COL1A1 as an Underlying Cause of Ehlers–Danlos Syndrome: A Report of a Saudi Founder Mutation. Global Medical Genetics, 7(4), 109-112.

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Illumina RNA expression profiling

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cDNA was synthesized and amplified from 40 ng RNA using the Ovation Pico WTA system V2 (NuGEN) and purified using the MiniElute Reaction Cleanup Kit (Qiagen). Yield and purity were measured using the 2100 Bioanalyser instrument and the RNA 6000 Nano kit (Agilent). Four microgram of amplified cDNA was biotin labeled with Encore Biotin Module (NuGen), purified, concentrated and hybridized onto Illumina HumanHT-12 v4 Expression BeadChip array and scanned using the Illumina iScan platform. The data was then subjected to QC analysis and normalization using Illumina's Genome Studio Suite v1.0.

Ramadani F., Bowen H., Gould H.J, & Fear D.J. (2019). Transcriptional Analysis of the Human IgE-Expressing Plasma Cell Differentiation Pathway. Frontiers in Immunology, 10, 402.

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Genotyping ESR1 Variants for AD Risk

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Genomic DNA was extracted from total peripheral blood leukocytes using standard methods. We used a multistep selection process to identify candidate SNPs for genotyping. We first selected SNPs within ESR1 that were previously reported to be associated with an increased incidence or earlier age at onset of AD in any population. We then referenced the International HapMap Project (www.hapmap.org) to select tagging SNPs in both Caucasian and African populations. To provide sufficient coverage of the gene, we selected SNPs to maintain a pairwise r² threshold of 0.8 in SNPs with a minimum minor allele frequency of 0.2. We obtained an average intermarker distance of approximately 6.2 kilobase pairs between SNPs, which provided good coverage of the gene as viewed on linkage disequilibrium maps (Supplementary Figures 1-3).
Forty-one ESR1 SNPs as well as 100 ancestry informative markers (AIMs) were genotyped in a total of 1,436 samples using Illumina GoldenGate custom panels and the Illumina IScan platform. Genotyping was performed according to standard protocols (www.Illumina.com). The complete list of ESR1 SNPs that were genotyped, along with their minor allele frequencies (MAF) by self-identified ethnicity, is presented in Table 3. Duplicate genotyping was performed on ten percent of samples to verify accuracy, and the concordance rate was greater than 97 percent.

Janicki S.C., Park N., Cheng R., Clark L.N., Lee J.H, & Schupf N. (2014). ERα Variants Affect Age at Onset of Alzheimer's Disease in a Multiethnic Female Cohort. Dementia and geriatric cognitive disorders, 38(0), 200-213.

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