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Beadxpress reader

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The BeadXpress Reader is a fluorescence-based instrument designed for high-throughput genetic analysis. It is capable of detecting and quantifying fluorescently labeled DNA or RNA samples. The BeadXpress Reader is intended for use in research and development applications.

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Lab products found in correlation

Ez dna methylation gold kit, by Zymo Research (3 mentions) Infinium humanmethylation27 beadchip, by Illumina (3 mentions) Veracode goldengate assay, by Illumina (3 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Veracode technology, by Illumina (2 mentions) Qiaamp 96 spin blood kit, by Qiagen (2 mentions) Goldengate genotyping assay system, by Illumina (2 mentions) Genomestudio data analysis software v2011, by Illumina (2 mentions) Genomestudio software, by Illumina (2 mentions) Quant it picogreen kit, by Thermo Fisher Scientific (1 mentions) Synergy 2 plate reader, by Agilent Technologies (1 mentions) Genomestudio software v2011, by Illumina (1 mentions) Goldengate genotyping assay for veracode manual protocol, by Illumina (1 mentions) Veracode genotyping assay, by Illumina (1 mentions) Genomestudio v2011, by Illumina (1 mentions) Humanomni2.5 8 platform, by Illumina (1 mentions) Gentra autopure robot, by Qiagen (1 mentions) Qiaamp dna extraction kit, by Qiagen (1 mentions) Genomestudio data analysis software, by Illumina (1 mentions) Oragene dna sample collection kit, by DNA Genotek (1 mentions)

18 protocols using beadxpress reader

1

DNA Methylation Profiling Using Illumina Beadchips

Cited 2 times
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DNA was isolated from peripheral blood leukocytes obtained from stored blood samples, and was bisulfite-converted with the EZ DNA Methylation Gold Kit (Zymo Research, Orange CA). Bisulfite-converted DNA samples were whole-genome amplified, enzymatically fragmented, and purified, then hybridized to Illumina Infinium HumanMethylation27BeadChips, which contain locus-specific DNA oligomers and a set of 56 control probes. The array was then fluorescently stained, scanned using the Illumina BeadXpress reader, and assessed for fluorescence intensities across the methylated and unmethylated bead types at 27,578 CpG sites [31 (link)–33 (link)]. This work was performed at the Genotyping Core in the Mayo Clinic Advanced Genomics Technology Center (Rochester, MN).
Smith J.A., Zagel A.L., Sun Y.V., Dolinoy D.C., Bielak L.F., Peyser P.A., Turner S.T., Mosley TH J.r, & Kardia S.L. (2014). Epigenomic Indicators of Age in African Americans. Hereditary genetics : current research, 3(3), 137.
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2

Genome-Wide Association Study of Rice BB Resistance

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120 JMAGIC lines were selected and phenotyped by measuring lesion length of leaves inoculated with BB race K3a. The Infinium 6K Bead Chip was used for genotyping the tested lines. The SNP chips were composed of 384-SNP sets customized for indica-japonica SNP chip (ID: GS0011862-OPA), and the results were scanned using the Illumina BeadXpress Reader (Genotyping services Lab, IRRI). GWAS analysis was carried out based on a mixed linear model (MLM) using genome association and prediction integrated tool (GAPIT) in R [26 (link)]. PCA.total = 3 was applied as number of principal components (PCs) to use to control for population structure.
Kim S.M, & Reinke R.F. (2019). A novel resistance gene for bacterial blight in rice, Xa43(t) identified by GWAS, confirmed by QTL mapping using a bi-parental population. PLoS ONE, 14(2), e0211775.
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3

Constructing Genetic Linkage Maps from F2 Plants

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Whole genomic DNA was extracted from leaf tissue from each F2 plant as well as the mapping parents using a modified CTAB protocol [44 ]. DNA concentrations were estimated using the Quant-iT PicoGreen kit (Invitrogen) using a Biotek Synergy 2 plate reader (Winooski, VT). The Illumina GoldenGate Assay described above was then used to genotype each sample on the BeadXpress Reader (Illumina) at the Georgia Genomics Facility. Allele calls were obtained using the Illumina GenomeStudio software v2011.1.
A genetic linkage map was constructed using MapMaker 3.0/EXP [45 (link),46 (link)]. Briefly, initial linkage groups (LGs) were identified using the “group” command with a minimum LOD score of 5.0 and a maximum frequency of recombination of 0.4 between adjacent markers. Preliminary map orders were determined using the “compare” command on a subset of markers within LGs and the remaining markers were placed using the “try” command. For each LG, marker orders were confirmed using the “ripple” command and the final marker orders, presented here, represent the most likely marker orders given the data.
Pearl S.A., Bowers J.E., Reyes-Chin-Wo S., Michelmore R.W, & Burke J.M. (2014). Genetic analysis of safflower domestication. BMC Plant Biology, 14, 43.
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4

High-Throughput SNP Genotyping of F2 Plants

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Genomic DNA of all the F2 plants and the parents was extracted from 18 to 21-day-old seedlings using the CTAB technique of Murray and Thompson (1980) (link) with a few modifications. The final concentration of the DNA samples was normalized to 50 ng/μl. Genotyping was performed using the Illumina BeadXpress 384-plex SNP plates with the oligo pool assay (OPA) customized for Indica–Indica (Illumina OPA ID: GS0011861-OPA; RiceOPA2.1) (Thomson et al. 2012 ). PCR amplification and hybridization were performed using the GoldenGate genotyping assay for VeraCode manual protocol (Illumina, San Diego, CA, USA). The VeraCode 384-plex plate was scanned using the Illumina BeadXpress Reader (Genotyping Services Lab, IRRI) and raw intensity values were exported from the GenomeStudio software V1.1.0 (Illumina). Genotype calling was performed using Alchemy software (Wright et al. 2010 (link)).
Baltazar M.D., Ignacio J.C., Thomson M.J., Ismail A.M., Mendioro M.S, & Septiningsih E.M. (2019). QTL mapping for tolerance to anaerobic germination in rice from IR64 and the aus landrace Kharsu 80A. Breeding Science, 69(2), 227-233.
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5

Genotyping HIV+ and HIV- Blood Samples

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DNA was extracted from 200 μl of packed blood pellets from HIV+ patients and whole-blood samples from HIV− donors using the QIAamp 96 spin blood kit (QIAGEN, Valencia, CA). DNA concentrations were measured using Qubit® Fluorometer (Invitrogen, Carlsbad, CA). SNPs were genotyped using Illumina’s GoldenGate® genotyping assay system combined with VeraCode® Technology (Illumina Inc., San Diego, CA). Allelic discrimination was performed using a BeadXpress® Reader (Illumina) according to the manufacturer’s instructions.
The genotype data were uploaded and filtered using the GenomeStudio data analysis software v2011.1 (Illumina Inc., San Diego, CA). SNPs were filtered by genotype call frequency (<0.9, n = 1) and replicate errors (n = 2). Samples with genotype call frequency <0.9 were excluded (n = 4). Subsequently, SNPs were excluded from analysis if genotypic distribution among HIV− donors, stratified by race, deviated from the Hardy-Weinberg equilibrium (HWE) with a significant cutoff value of P ≤ 0.001 (n = 1). Thus, in the final analysis, 41 SNPs, as listed in Supplementary Table A, were examined in a total of 276 subjects (HIV+, n = 180; HIV−, n = 96).
Willie B., Hall N., Stein C., Jurevic R., Weinberg A., Mehlotra R, & Zimmerman P. (2014). Association of toll-like receptor polymorphisms with HIV status in North Americans. Genes and immunity, 15(8), 569-577.
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6

Pharmacogenomic Assessment of Cytochrome P450 Variants

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Among patients who consented, DNA was extracted and 6 loss of function (LOF) or decrease of function (DOF) SNPs, in CYP2A6 (rs28399433 [risk allele C]), CYP2B6 (rs28399499 [G], rs35303484 [G], rs35979566 [A], rs3745274 [A]), and CYP3A4 (rs4646437 [A]) were assessed using the Illumina VeraCode™ Genotyping Assay. The BeadArrays were scanned in an Illumina BeadXpress™ reader and the fluorescent signals analyzed with Illumina GenomeStudio software, with automated genotype clustering and calling. A genetic risk score from 1 (lowest risk) to 6 (highest risk) based on the presence of LOF and DOF SNPs was defined a priori (Lubomirov et al., 2011 (link)) and calculated for each participant (Table 1).
Cummins N.W., Neuhaus J., Chu H., Neaton J., Wyen C., Rockstroh J.K., Skiest D.J., Boyd M.A., Khoo S., Rotger M., Telenti A., Weinshilboum R, & Badley A.D. (2015). Investigation of Efavirenz Discontinuation in Multi-ethnic Populations of HIV-positive Individuals by Genetic Analysis. EBioMedicine, 2(7), 706-712.
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7

Genotyping Domestic and Przewalski Horses

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A VeraCode GoldenGate assay (Illumina) was designed targeting 384 SNPs that were called in the resequencing samples. A total of 200 domestic horses, one Przewalski’s horse and five other equids were genotyped using the standard protocol. The GoldenGate assays were read using a BeadXpress Reader (Illumina), and data were analyzed on GenomeStudio v2011.1 software (Illumina). SNPs located outside the non-dun2 deletion with a call rate of less than 80% (17 SNPs) or invariable in typed individuals (one SNP) were excluded from the analysis. The three SNPs within the deleted region had a call rate of 67–68%, consistent with one-third of the samples being homozygous for the non-dun2 deletion. All samples used had call rates of no less than 97% (domestic horses) or 90% (other equids).
Imsland F., McGowan K., Rubin C.J., Henegar C., Sundström E., Berglund J., Schwochow D., Gustafson U., Imsland P., Lindblad-Toh K., Lindgren G., Mikko S., Millon L., Wade C., Schubert M., Orlando L., Penedo M.C., Barsh G.S, & Andersson L. (2015). Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses. Nature genetics, 48(2), 152-158.
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8

DNA Methylation Profiling of AA Cohort

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Peripheral blood leukocytes were isolated from stored blood samples of 1,008 Phase II AA participants and used to measure DNAm levels. The EZ DNA Methylation Gold Kit (Zymo Research, Orange, CA) was used for bisulfite conversion. The methylation assay was performed at the Mayo Clinic Advanced Genomics Technology Center using Illumina® Infinium HumanMethylation27 BeadChips and Illumina BeadXpress reader. As a quality control, seven samples were excluded from analysis due to poor bisulfite conversion efficiency (intensity <4,000). An additional 28 samples were removed because of poor background signals, leaving a total of 973 samples. The lumi package (Du, Kibbe, & Lin, 2008 (link)) in R software was used for background adjustment, color balance adjustment, and quantile normalization. Thirty samples were removed because <95% of probes had a detection p value <.01, and two were excluded because the predicted gender based on DNA methylation did not match with the reported gender, leaving a total of 941 samples. Analyses for this study were conducted on participants who had completed clinical, genotyping, and DNAm data (Figure 1, N = 739).
Wright M.L., Ware E.B., Smith J.A., Kardia S.L, & Taylor J.Y. (2018). Joint Influence of SNPs and DNA Methylation on Lipids in African Americans From Hypertensive Sibships. Biological Research for Nursing, 20(2), 161-167.
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9

DNA Methylation Profiling Using Illumina Beadchips

Cited 2 times
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DNA was isolated from peripheral blood leukocytes obtained from stored blood samples, and was bisulfite-converted with the EZ DNA Methylation Gold Kit (Zymo Research, Orange CA). Bisulfite-converted DNA samples were whole-genome amplified, enzymatically fragmented, and purified, then hybridized to Illumina Infinium HumanMethylation27BeadChips, which contain locus-specific DNA oligomers and a set of 56 control probes. The array was then fluorescently stained, scanned using the Illumina BeadXpress reader, and assessed for fluorescence intensities across the methylated and unmethylated bead types at 27,578 CpG sites [31 (link)–33 (link)]. This work was performed at the Genotyping Core in the Mayo Clinic Advanced Genomics Technology Center (Rochester, MN).
Smith J.A., Zagel A.L., Sun Y.V., Dolinoy D.C., Bielak L.F., Peyser P.A., Turner S.T., Mosley TH J.r, & Kardia S.L. (2014). Epigenomic Indicators of Age in African Americans. Hereditary genetics : current research, 3(3), 137.
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10

Genome-Wide SNP Profiling with Illumina

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Genotyping was performed using Illumina Human Omni2.5-8 platform. The HumanOmni2.5-8 BeadChip delivers comprehensive coverage of both common and rare SNP content from the 1000 Genomes Project (1kGP; MAF > 2.5 %), designed to be maximally informative for diverse world populations. It is able to identify 2,379,855 polymorphisms. The scan protocol followed the standard Illumina procedures using Illumina BeadXpress Reader. The microarray data was analyzed with GenomeStudio V2011.1 and GT module 1.9.4 using default analysis settings. Each SNP is analyzed independently to cluster and identify genotypes. Genotype calls are generated by comparing experimental data with those in the supplied cluster file(*.egt). Calls are generally highly accurate and unambiguous for high quality samples.
Cocchi E., Fabbri C., Han C., Lee S.J., Patkar A.A., Masand P.S., Pae C.U, & Serretti A. (2016). Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway. BMC Psychiatry, 16, 106.
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