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GenomeStudio specifications

Information


Unique identifier OMICS_00854
Name GenomeStudio
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use License purchase required
Biological technology Illumina
Operating system Unix/Linux
License Commercial
Computer skills Medium
Version 2011.1
Stability Stable
Maintained Yes

Subtool


  • cnvPartition

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Versioning


No version available

Documentation


Additional information


https://support.illumina.com/downloads/genomestudio-2011-1-user-guides.html

GenomeStudio citations

 (678)
library_books

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

2018
Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] e Illumina Infinium MethylationEPIC Beadchip. Integragen SA (Evry, France) carried out microarray experiments and hybridized to the BeadChip arrays following the manufacturer’s instructions. Illumina GenomeStudio software was used to extract the probe DNA methylation intensity signal values for each locus. Data were then preprocessed following recommendations from the Dedeurwaerder et al. Data wer […]

library_books

Translational study identifies XPF and MUS81 as predictive biomarkers for oxaliplatin based peri operative chemotherapy in patients with esophageal adenocarcinoma

2018
Sci Rep
PMCID: 5940885
PMID: 29739952
DOI: 10.1038/s41598-018-24232-2

[…] Fisher Scientific, Waltham, MA). Extracted mRNA samples were hybridised to Illumina HumanHT-12-v3 Expression BeadChips (Illumina, San Diego, CA). Raw gene expression data was processed using Illumina GenomeStudio software (v1.6) to generate expression intensities which were considered in a logged base 2 scale. Data were then analysed using R statistical software (v2.15) (http://www.Rproject.org) ( […]

library_books

Mice lacking the transcriptional regulator Bhlhe40 have enhanced neuronal excitability and impaired synaptic plasticity in the hippocampus

2018
PLoS One
PMCID: 5929507
PMID: 29715265
DOI: 10.1371/journal.pone.0196223

[…] ubated 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. […]

library_books

Metabolic and inflammatory biomarkers are associated with epigenetic aging acceleration estimates in the GOLDN study

2018
Clin Epigenetics
PMCID: 5907301
PMID: 29713391
DOI: 10.1186/s13148-018-0481-4

[…] ads []. Cells were lysed and DNA was extracted using DNeasy kits (Qiagen, Venlo, Netherlands). After following standard Illumina protocols, the resulting intensity files were analyzed with Illumina’s GenomeStudio to generate beta scores representing the percent of methylated sites at that location across all the cells in a sample. After previously reported QC, methylation data were available for 4 […]

library_books

Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation

2018
PLoS Biol
PMCID: 5927466
PMID: 29668680
DOI: 10.1371/journal.pbio.2005707

[…] ial methylation at the CpG dinucleotide level was conducted using Human Methylation450 v1 BeadChip arrays (Illumina) following the InfiniumHD methylation protocol. Data were obtained using Illumina’s GenomeStudio software (version 2011.1) using no background subtraction and no normalization parameters. Probes in a probe × cell × time block with >1 failed reads or >1 outliers (1.5 IQR rule on resid […]

library_books

Tools for Genetic Studies in Experimental Populations of Polyploids

2018
Front Plant Sci
PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] he two main service providers for high-density SNP arrays, Illumina and Affymetrix, both offer proprietary software solutions for analyzing polyploid datasets. Affymetrix’s Power Tools and Illumina’s GenomeStudio (with its Polyploid Genotyping Module) have both been developed with both diploid and polyploid datasets in mind. However, there have also been a number of genotyping tools that have been […]

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GenomeStudio institution(s)
Illumina, San Diego, CA, USA

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