IScan protocols

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IScan specifications

Information


Unique identifier OMICS_11555
Name IScan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andreas Wagner <>

Publication for IScan

IScan in pipelines

 (5)
2017
PMCID: 5567664
PMID: 28830357
DOI: 10.1186/s12864-017-3979-9

[…] complete pin184 population were custom genotyped with the infinium 8303 potato array (8.3 k solcap snp array) at the life & brain center (department of genomics, bonn, germany) on an illumina iscan system, applying the infinium assay. the genotypes of bi-allelic snp markers in the pin184 population were called using the software package ‘fittetra’ []. the package was run using […]

2016
PMCID: 4872231
PMID: 27192970
DOI: 10.1038/srep26424

[…] hybridized to the array chips, followed by staining and processing of the single-base extension using hm450 beadchip kit (illumina) according to the manufacturer’s instructions. chips were imaged by iscan (illumina). methylation profiling was performed on the samples from the same individuals in the same batch., quality assessment and quality control of reads were evaluated using fastqc […]

2015
PMCID: 4312029
PMID: 25635822
DOI: 10.1371/journal.pone.0116845

[…] a capillary flow-through chamber. non-specific dna was washed away and then stained for single base extension of the oligonucleotides present on the chip. all beadchips were scanned on the illumina iscan at the institute of child health, university college london. ncbi build 36 (hg18) mapping was used., to select for polymorphic snps for subsequent linkage analysis, a hardy-weinberg filter […]

2015
PMCID: 4397063
PMID: 25875648
DOI: 10.1371/journal.pone.0123872

[…] annotation, filtering and interpretation of the variants was done using variantdb []., illumina snp-array data were previously obtained from 30 samples using a humancytosnp-12 v2.1 beadchip on an iscan system, following standard protocols as provided by the manufacturer (illumina). snp genotypes were extracted from illumina genomestudio (v2011.1) using the genotyping module (v.1.9.4). […]

2012
PMCID: 3342946
PMID: 22258146
DOI: 10.4161/rna.9.1.18121

[…] of labeled crnas were hybridized onto human or rat beadchips, respectively, using the illumina whole genome gene expression direct hybridization protocol. the beadchips were scanned using illumina iscan and the raw data were generated by genomescan software (illumina). the raw data were then log2 transformed and quantile normalized without background subtraction. anova statistical tests […]


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IScan in publications

 (952)
PMCID: 5954162
PMID: 29765130
DOI: 10.1038/s41598-018-25827-5

[…] history of diagnosed cardiovascular disease at the time of recruitment. (see supplementary information for more details). dna samples were run on the cardio-metabochip and scanned on the illumina® iscan platform by agresearch limited (invermay, new zealand)., quality control with summary analysis of allele and genotype frequencies, hardy-weinberg equilibrium tests, and missing genotype rates […]

PMCID: 5945586
PMID: 29760939
DOI: 10.1038/s41439-018-0004-z

[…] dna samples was performed using the humancytosnp-12 dna analysis beadchip kit (illumina, san diego, ca, usa) according to the manufacturer’s protocols. the snp arrays were scanned using the illumina iscan system, and the data were analyzed with illumina’s karyostudio (version 1.4) using the default cnvpartition algorithm settings (version 3.0.7, illumina)., sequencing was performed on the ii-2, […]

PMCID: 5932008
PMID: 29720645
DOI: 10.1038/s41467-018-04126-7

[…] × 28.8 visual degrees. the fixation spot size was 0.25° in diameter. all images were presented in random order using custom software. eye position was monitored using an infrared eye tracking system (iscan). juice reward was delivered every 2–4 s if fixation was properly maintained. custom software (kofiko) was used to present visual stimuli, track fixation, deliver juice, and synchronize stimulus […]

PMCID: 5929507
PMID: 29715265
DOI: 10.1371/journal.pone.0196223

[…] ref8 v2 beadchip microarrays (illumina, san diego, ca). following post-hybridization rinses, arrays were incubated with streptavidin-conjugated cy3, and scanned at 0.53 microns using an illumina iscan scanner. hybridization intensity data were extracted from the scanned images, and evaluated using illumina genomestudio software, v2011.1., raw microarray florescent signal data were filtered […]

PMCID: 5946024
PMID: 29780395
DOI: 10.3389/fpls.2018.00573

[…] from young leaf tissues by the ctab method (). the 198 rils and two parents were genotyped using the wheat 90k iselect array with 81,587 snp (). genotyping assays were carried out on the illumina iscan reader and made genotypic clusters for each snp using genomestudio software 1.9.4 (illumina; http://www.illumina.com)., prior to mapping, snp data were evaluated following . snps […]


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IScan institution(s)
Department of Biochemistry, University of Zurich, Zurich, Switzerland; Department of Biology, University of New Mexico, Albuquerque, NM, USA
IScan funding source(s)
Support through SNF grant 315200-116814 and through the Santa Fe Institute is gratefully acknowledged.

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