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GenomeStudio computational protocol

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

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Additional information


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

GenomeStudio IN pipelines

 (27)
2017
PMCID: 5435826
PMID: 28573109
DOI: 10.3389/fcimb.2017.00193

[…] raw and normalized data are available at ncbi gene expression omnibus repository under accession number gse58291. qc checks for sample-independent and sample-dependent controls were performed in genomestudio version 3.1 (illumina inc.) and data exported to lumi in bioconductor in r for analysis (du et al., 2008). pairwise comparisons were defined as bk or fk vs. controls, and bk vs. fk. […]

2017
PMCID: 5603607
PMID: 28924151
DOI: 10.1038/s41598-017-12084-1

[…] beadchip, following the illumina infinium hd methylation protocol. the chip was analyzed using illumina hiscan sq fluorescent scanner and the intensities of the images were extracted using genomestudio (2010.3) methylation module (1.8.5) software. a three-step-based normalization procedure was performed using the lumi35 package available for bioconductor36 in the r statistical […]

2017
PMCID: 5610037
PMID: 28942197
DOI: 10.1016/j.redox.2017.09.006

[…] dorset, uk), according to manufacturer's instructions. after staining, the beadchips were scanned on an illumina beadarray reader with bead scan software (illumina)., following the beadchip scan, genomestudio software (illumina) was used to produce bead summary data from the raw data, which was exported as a custom report using the ‘arrayexpress data submission report plug-in v2.0.0’. […]

2017
PMCID: 5643418
PMID: 29075261
DOI: 10.3389/fimmu.2017.01276

[…] technologies). 50 ng of rna was used for hybridization into illumina ht-12v4 bead-arrays (illumina inc.) at the wellcome trust sanger institute, uk, and fluorescent probe intensities captured with genomestudio software (illumina inc.)., differential gene transcription was assessed by analysis of changes in transcript abundance in whole-blood samples collected during the study. raw data […]

2016
PMCID: 4896498
PMID: 27272489
DOI: 10.1371/journal.pone.0156594

[…] on sex-specific signatures in the first step. after excluding potentially mixed-up samples, 1092 samples with gene expression data available at bl and fu were kept for further analysis., illumina genomestudio built-in function for detecting expressed probes was compared with the corresponding function from beadarray r package [19]. both methods use negative control probes to consider […]

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