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Genomestudio platform

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The GenomeStudio platform is a software tool designed for the analysis and visualization of data generated from Illumina's next-generation sequencing (NGS) technologies. It provides a comprehensive suite of tools for data processing, quality control, and downstream analysis.

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Lab products found in correlation

Ez dna methylation kit, by Zymo Research (2 mentions) Infinium methylationepic beadchip array, by Illumina (2 mentions) Humanomniexpress, by Illumina (1 mentions) Mousewg 6 v2.0 expression beadchip, by Illumina (1 mentions) Genotyping array, by Illumina (1 mentions) Humanhap610 quad beadchip, by Illumina (1 mentions) Cytoscan hd, by Thermo Fisher Scientific (1 mentions) Human core exome, by Thermo Fisher Scientific (1 mentions)

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GenomeStudio (603 citations)

8 protocols using genomestudio platform

1

Genome-wide DNA Methylation Analysis of Scleroderma Fibroblasts

Cited 1 time
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Genomic DNA from five patients with diffuse cutaneous SSc was isolated from PBS- and DZNep (5 μM)-treated dermal fibroblasts, and subsequently, bisulfite converted using an EZ DNA Methylation kit (Zymo Research). Genome-wide DNA methylation was evaluated using the Illumina Infinium MethylationEPIC BeadChip Array, which allows measuring DNA methylation levels in over 850,000 CpG sites across the genome, and covers 27,364 annotated genes. The array also covers enhancers, regions of open chromatin identified by ENCODE project, DNase hypersensitive sites, and miRNA promoter regions. Analysis was performed using the Illumina GenomeStudio platform as described (28 (link)). The average level of DNA methylation (β) on each CpG site was compared between PBS- and DZNep-treated samples. Differentially methylated CpG sites were defined as those with a differential methylation score ≥|22| (equivalent to P value of less than 0.01 after adjusting for multiple testing) and a mean methylation difference greater than 10% between the two groups. Differentially methylated genes were analyzed for Gene Ontology (GO), network, and pathway enrichments using the Database for Annotation, Visualization, and Integrated Discovery (DAVID V.6.7) (29 (link), 30 (link)).
Tsou P.S., Campbell P., Amin M.A., Coit P., Miller S., Fox D.A., Khanna D, & Sawalha A.H. (2019). Inhibition of EZH2 prevents fibrosis and restores normal angiogenesis in scleroderma. Proceedings of the National Academy of Sciences of the United States of America, 116(9), 3695-3702.
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2

Comprehensive Genetic Profiling via Illumina

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Customer saliva sample accessioning, DNA extraction, and genotyping were completed by the Illumina FastTrack Microarray Services labs. Customer genotype data for this study was generated using the Illumina Human OmniExpress platform. This genotyping array assays 730,525 SNPs (709,358 SNPs are on autosomal chromosomes) and small indels across the genome. The SNPs on this array were carefully selected to capture the majority of common genetic variation in European and other worldwide populations. (Note that genotype data on sex-linked chromosomes are not used in this study). Genotypes were called by Illumina technicians using the GenomeStudio platform.
Han E., Carbonetto P., Curtis R.E., Wang Y., Granka J.M., Byrnes J., Noto K., Kermany A.R., Myres N.M., Barber M.J., Rand K.A., Song S., Roman T., Battat E., Elyashiv E., Guturu H., Hong E.L., Chahine K.G, & Ball C.A. (2017). Clustering of 770,000 genomes reveals post-colonial population structure of North America. Nature Communications, 8, 14238.
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3

Retinal Gene Expression Profiling in Mouse Models

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Triplicate RNA samples were prepared from 4 pooled retinas from 1 male and 1 female mouse at P10 for WT and homozygous E168d2neo, R90Wneo and −/− mice. The RNA was fluorescent labeled and hybridized to MouseWG-6 v2.0 Expression Beadchips (Illumina) by Washington University Genome Technology Access Center (GTAC). The raw microarray datasets are available at the NCBI GRO website (http://www.ncbi.nlm.nih.gov/gds, access number: GSE51184). Microarray data were analyzed using significance analysis of microarrays (SAM) following background subtraction and quantile normalization in Illumina Genome Studio platform. Control probes and probes with detection p-value <0.05 across all samples were removed prior to any analysis. Candidate probes with 2.0-fold disregulation at false discovery rate ≤0.05 from each comparison were chosen for further analysis. Cellular processes associated with differentially expressed genes were assigned based on gene ontology provided by Mouse Genome Informatics (http://www.informatics.jax.org/).
Tran N.M., Zhang A., Zhang X., Huecker J.B., Hennig A.K, & Chen S. (2014). Mechanistically Distinct Mouse Models for CRX-Associated Retinopathy. PLoS Genetics, 10(2), e1004111.
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4

Illumina SNP Genotyping Protocol

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SNP variants were called by technicians at the Illumina FastTrack Microarray Services lab using the GenomeStudio platform. Genotype data were generated using an Illumina genotyping array with approximately 730,000 SNPs. During the four years of sample collection, two versions of the array were used for genotyping. All downstream analyses used the intersection of SNPs present on both versions of the chip. We included chip version as a covariate in all association mapping models.
Wright K.M., Rand K.A., Kermany A., Noto K., Curtis D., Garrigan D., Slinkov D., Dorfman I., Granka J.M., Byrnes J., Myres N., Ball C.A, & Ruby J.G. (2019). A Prospective Analysis of Genetic Variants Associated with Human Lifespan. G3: Genes|Genomes|Genetics, 9(9), 2863-2878.
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5

Genome-wide DNA Methylation Analysis of EZH2-overexpressing CD4+ T Cells

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Genomic DNA, which was isolated from control and EZH2-overexpressing naïve CD4+ T cells from 4 healthy subjects with and without stimulation, was bisulfite converted using an EZ DNA Methylation kit (Zymo Research). Genome-wide DNA methylation status in these samples was then evaluated using the Illumina Infinium Methylation EPIC BeadChip Array. The Illumina GenomeStudio platform was used to analyze the methylation data as previously described (4 (link)). The average level of DNA methylation (β) on each CpG site was compared between control and EZH2-overexpressing samples. Differentially methylated CpG sites were defined as those with a differential methylation score ≥|22| (equivalent to p value of less than 0.05 after adjusting for multiple testing) and a mean methylation difference greater than 10% between the 2 groups. Differentially methylated genes were analyzed for Gene Ontology (GO), network, and pathway enrichments using the Database for Annotation, Visualization and Integrated Discovery (DAVID V.6.7) (12 (link), 13 (link)).
Tsou P.S., Coit P., Kilian N.C, & Sawalha A.H. (2017). EZH2 modulates the DNA methylome and controls T cell adhesion through junctional adhesion molecule-A in lupus patients. Arthritis & rheumatology (Hoboken, N.J.), 70(1), 98-108.
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6

Genome-wide SNP analysis to identify pathogenic CNVs

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Genome wide SNP microarray was performed on all available affected and normal individuals of the eight families (n = 41) by using Illumina’s Infinium Human CoreExome-24v1.3 kit (551,004 fixed markers, including ~ 284,000 SNPs (~ 1 marker every 6 Kb)), according to the manufacturer’s protocol and the Illumina GenomeStudio platform (Illumina CoreExome) was used for data processing. The SNP data was exported into PLINK format for analysis with HomozygosityMapper [15 (link)] to identify homozygous by descent (HBD) regions. For each HBD region, genotype tables were checked to confirm homozygosity and haploidentity. False positive data was excluded from downstream analysis. In case of X-Chromosome, HBD regions were identified by manual curation on genotype data and regions spanning more than 1 Mb were selected. CNV analysis was performed by using Illumina GenomeStudio cnvPartition plugin to identify likely pathogenic homozygous or heterozygous CNVs. For validation of CNV, qPCR was performed by using primers designed from within the CNV and its flanking region. Breakpoints were identified by designing overlapping primers from the flanking regions of CNV and the amplified DNA fragment was subjected to Sanger sequencing.
Rasheed M., Khan V., Harripaul R., Siddiqui M., Malik M.A., Ullah Z., Zahid M., Vincent J.B, & Ansar M. (2021). Exome sequencing identifies novel and known mutations in families with intellectual disability. BMC Medical Genomics, 14, 211.
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7

Genotyping with HumanHap 610-Quad

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Samples were genotyped on the HumanHap 610-Quad Beadchip (Illumina, Inc.) and contemporaneously processed at the same laboratory. Raw probe intensity data were processed according to the manufacturer’s guidelines with the GenomeStudio platform (Illumina, Inc.) to obtain the normalized probe intensity at each marker and the log R ratio and B allele frequency at each marker.
Rucker J.J., Tansey K.E., Rivera M., Pinto D., Cohen-Woods S., Uher R., Aitchison K.J., Craddock N., Owen M.J., Jones L., Jones I., Korszun A., Barnes M.R., Preisig M., Mors O., Maier W., Rice J., Rietschel M., Holsboer F., Farmer A.E., Craig I.W., Scherer S.W., McGuffin P, & Breen G. (2016). Phenotypic Association Analyses With Copy Number Variation in Recurrent Depressive Disorder. Biological Psychiatry, 79(4), 329-336.
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8

Autozygosity Mapping Using Microarray Data

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Autozygosity mapping was performed using microarray data from the Illumina Human CoreExome, Affymetrix Mapping 500K NspI, Affymetrix CytoScan HD and Affymetrix SNP 5.0 or 6.0. All genotyping was performed according to the manufacturer's protocol, and data were processed using either the Affymetrix Genotyping Console (500K and 5.0), Affymetrix ChAS Software Suite (CytoScan HD and SNP 6.0) or the Illumina GenomeStudio platform (Illumina CoreExome). All data were exported to PLINK format for analysis using HomozygosityMapper 25 and FSuite 26 . Details are provided in the Supplementary Methods.
Harripaul R., Vasli N., Mikhailov A., Rafiq M.A., Mittal K., Windpassinger C., Sheikh T.I., Noor A., Mahmood H., Downey S., Johnson M., Vleuten K., Bell L., Ilyas M., Khan F.S., Khan V., Moradi M., Ayaz M., Naeem F., Heidari A., Ahmed I., Ghadami S., Agha Z., Zeinali S., Qamar R., Mozhdehipanah H., John P., Mir A., Ansar M., French L., Ayub M, & Vincent J.B. (2018). Mapping autosomal recessive intellectual disability: combined microarray and exome sequencing identifies 26 novel candidate genes in 192 consanguineous families. Molecular psychiatry, 23(4).
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