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Beadstudio

Manufactured by Illumina
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BeadStudio is a data analysis software developed by Illumina. It is designed to process and analyze data generated from Illumina's BeadChip arrays, which are used for various genomic applications such as genotyping, copy number variation analysis, and methylation profiling. The software provides tools for data visualization, quality control, and statistical analysis.

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Lab products found in correlation

Beadarray reader, by Illumina (5 mentions) Totalprep rna amplification kit, by Thermo Fisher Scientific (5 mentions) Dneasy blood tissue kit, by Qiagen (4 mentions) Human1m duo dna analysis beadchip, by Illumina (4 mentions) Trizol reagent, by Thermo Fisher Scientific (4 mentions) Beadstation 500 beadarray reader, by Illumina (3 mentions) Birdsuite, by Thermo Fisher Scientific (3 mentions) Beadscan, by Illumina (3 mentions) Gentra puregene, by Qiagen (2 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) Rneasy plus mini kit, by Qiagen (2 mentions) Messageamp premier rna amplification kit, by Thermo Fisher Scientific (2 mentions) Iscan scanner, by Illumina (2 mentions) Messageamp 3 rna amplification kit, by Thermo Fisher Scientific (2 mentions) Custom error model, by Illumina (2 mentions) Humanomniexpress 12v1 beadchip, by Illumina (2 mentions) Rneasy mini kit, by Qiagen (2 mentions) Infinium 2 multisample assay, by Illumina (2 mentions) Bovinehd beadchip, by Illumina (2 mentions) Hiseq 2000, by Illumina (2 mentions)

Close spelling variants of this product

BeadStudio software (158 citations) BeadStudio 3.2 (32 citations) BeadStudio v3.1.3 (26 citations) BeadStudio Data Analysis Software (16 citations) BeadStudio genotyping software (13 citations) BeadStudio software suite (5 citations) BeadStudio 2.0 (4 citations) BeadStudio, version 3.0 (4 citations) BeadStudio/GenomeStudio software (4 citations) BeadStudio Application (3 citations)

124 protocols using beadstudio

1

Genotyping Quality Control Procedures

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Genotyping was performed using the Illumina 660W-Quad BeadChip at the Center for Genotyping and Analysis at the Broad Institute, Cambridge, MA. This platform consists of 561,490 SNPs and 95,876 intensity-only probes. In addition to 3347 patient DNA samples, 58 blind duplicates, and 37 Coriell controls were genotyped. The Coriell controls include 1 trio (3 unique samples) that was duplicated on each plate. Genotyping calls were made using BeadStudio version 3.3.7 (2010).
Analysis tools used for quality control (QC) procedures included Illumina BeadStudio (2010), PLINK (Purcell et al., 2007 (link)), R (The R Development Core Team, 2007 ), STRUCTURE (Pritchard et al., 2000 (link)), and Eigenstrat in the Eigensoft package (Price et al., 2006 (link)). Data were cleaned using the QC pipeline developed by the eMERGE Genomics Working Group (Turner et al., 2011 (link)). This process includes evaluation of sample and marker call rate, gender mismatch and anomalies, duplicate and HapMap concordance, batch effects, Hardy-Weinberg equilibrium, sample relatedness, and population stratification. The data from all the patients, in addition to the HapMap II populations, were evaluated for population structure/substructure using Eigenstrat (Price et al., 2006 (link)). Of the 3347 unique samples, 3336 passed genotyping QC (see Supplementary Data and Figures S1–S3).
Kullo I.J., Shameer K., Jouni H., Lesnick T.G., Pathak J., Chute C.G, & de Andrade M. (2014). The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electronic medical record-based genome-wide association study. Frontiers in Genetics, 5, 166.
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2

Genome-wide genotyping of mouse populations

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All genome-wide genotyping was performed using the first, second, and third iterations of the Mouse Universal Genotyping Array, MUGA, MegaMUGA, and GigaMUGA (GeneSeek, Lincoln, NE) (Collaborative Cross Consortium 2012 (link); Morgan et al. 2015 (link)). Genotypes were called using Illumina BeadStudio (Illumina, Carlsbad, CA) and processed with Argyle (Morgan 2015 (link)). All genotypes are available at Zenodo (https://doi.org/10.5281/zenodo.377036).
Srivastava A., Morgan A.P., Najarian M.L., Sarsani V.K., Sigmon J.S., Shorter J.R., Kashfeen A., McMullan R.C., Williams L.H., Giusti-Rodríguez P., Ferris M.T., Sullivan P., Hock P., Miller D.R., Bell T.A., McMillan L., Churchill G.A, & de Villena F.P. (2017). Genomes of the Mouse Collaborative Cross. Genetics, 206(2), 537-556.
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3

Genome-Wide Methylation Analysis of HCC

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The genome-wide methylation data of an independent dataset (The Cancer Genome Atlas) consisting of 50 HCC samples and their matched surrounding tissues were employed. The Chip Analysis Methylation Pipeline (ChAMP) package is a pipeline which not only integrates currently available 450k analysis methods but also offers its own novel functionality. Statistical analyze of DNA genome methylation profile was performed on Illumina BeadStudio software (Genetech Biotech, Taipei, Taiwan). Β values were calculated during this procedure, obtained results were selected from 0 to 0.1 to represent CpG loci, and 0 to 100% on behalf of the percentage of methylation, respectively.
Chen W., Tang D., Tang D, & Dai Y. (2020). Epigenetic silencing of ZIC4 contributes to cancer progression in hepatocellular carcinoma. Cell Death & Disease, 11(10), 906.
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4

Genome-wide genotyping using GigaMUGA array

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Tail samples were sent to the University of North Carolina, where genomic DNA was extracted using a Qiagen Gentra Pure tissue kit according to the manufacturer's protocols. All genome-wide genotyping was performed using the GigaMUGA array at the University of North Carolina (GeneSeek, Lincoln, NE) [56 (link)]. Genotypes were called using Illumina BeadStudio (Illumina, Carlsbad, CA) and processed with argyle [57 (link)].
Veale A.J., Russell J.C, & King C.M. (2018). The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand. Royal Society Open Science, 5(1), 170879.
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5

SNP Genotyping of Brassica napus Cultivars

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Four young leaves from different individuals of each variety were planted in Wuhan and were sampled. DNA was extracted using a modified CTAB method27 and then adjusted to 50 ng μl−1. The 60K Brassica Infinium SNP array was employed and the SNP data were analyzed using Illumina BeadStudio (Illumina Inc. San Diego, California, USA).14 (link),20 (link),21 (link) The SNPs with call frequencies > 0.8 or minor allele frequencies (MAF) > 0.05 and homozygous genotype frequency > 0 were selected for association mapping analysis.20 (link) The physical position of the SNPs was identified by aligning the sequence of a 50 bp SNP probe attached to each SNP with the genome sequences of B. napus28 (link) using local BLASTn (BLAST: Basic Local Alignment Search Tool, http://blast.ncbi.nlm.nih.gov/Blast.cgi). If the SNP probe matched two or more locations in the reference genome, the SNPs were regarded as non-specific markers and abandoned.20 (link)
Wang X., Chen Y., Thomas C.L., Ding G., Xu P., Shi D., Grandke F., Jin K., Cai H., Xu F., Yi B., Broadley M.R, & Shi L. (2017). Genetic variants associated with the root system architecture of oilseed rape (Brassica napus L.) under contrasting phosphate supply. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 24(4), 407-417.
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6

Whole-Genome Sequencing and Genotyping

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Whole-genomic DNA was isolated from tissue samples using Qiagen Gentra Puregene or DNeasy Blood & Tissue kits according to the manufacturer's instructions. Genotyping was performed using either the Mega Mouse Universal Genotyping Array (MegaMUGA) or its successor, GigaMUGA (GeneSeek, Lincoln, NE). Genotypes were called using Illumina BeadStudio (Illumina Inc, Carlsbad, CA). Only samples with < 10% missing calls were retained for analysis. Sample sexes were confirmed by comparing the number of non-missing calls on the Y chromosome to the number of heterozygous calls on the X chromosome (Figure S1). New sequencing data was generated for 5 individuals (EC:FLO_STND:40_6255, EC:FLO_STND:40_3043, US:SEF_STND:40_3023, US:SEF_STND:40_3023, UK:INA_STND:40_278). Sequencing was performed at the University of North Carolina High Throughput Sequencing Facility. Whole genomic DNAs were sheared by ultrasonication and the resulting fragments were size selected to target size 350 bp using a PippinPrep system (Sage Sciences, Beverly, MA) .The UNC High Throughput Sequencing Facility generated sequencing libraries using Kapa DNA Library Preparation Kits (Kapa Biosystems, Wilmington, MA). Each library was run on its own lane of a HiSeq4000 (Illumina Inc, Carlsbad, CA), and generated 150 bp paired-end reads.
Morgan A.P., Hughes J.J., Didion J.P., Jolley W.J., Campbell K.J., Threadgill D.W., Bonhomme F., Searle J.B., & Villena F.P.d. (2022). Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales.
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7

Whole-Genome SNP Profiling of NSCLC

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Whole‐genome single nucleotide polymorphism array profiling was performed with 69 NSCLC cell lines and normal human bronchial epithelial cells using the Illumina Human1M‐Duo DNA Analysis BeadChip (Illumina). Data were processed using Illumina BeadStudio as described previously.5 Final copy number variations were interpreted qualitatively as deleted, unchanged or amplified.
Tanaka I., Sato M., Kato T., Goto D., Kakumu T., Miyazawa A., Yogo N., Hase T., Morise M., Sekido Y., Girard L., Minna J.D., Byers L.A., Heymach J.V., Coombes K.R., Kondo M, & Hasegawa Y. (2018). eIF2β, a subunit of translation‐initiation factor EIF2, is a potential therapeutic target for non‐small cell lung cancer. Cancer Science, 109(6), 1843-1852.
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8

Microarray Analysis of Liver Metastatic Cells

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Microarray analyses were performed using wild-type (WT) and highly liver metastatic (HM) SUIT-2 and PANC-1 cells. The Human WG-6 Expression BeadChip was used for analyses. We analyzed the datasets by using Illumina BeadStudio program. The datasets were uploaded to the GEO database (GEO accession: GSE144909).
Zheng B., Qu J., Ohuchida K., Feng H., Chong S.J., Yan Z., Piao Y., Liu P., Sheng N., Eguchi D., Ohtsuka T., Mizumoto K., Liu Z., Pervaiz S., Gong P, & Nakamura M. (2020). LAMA4 upregulation is associated with high liver metastasis potential and poor survival outcome of Pancreatic Cancer. Theranostics, 10(22), 10274-10289.
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9

Illumina BeadStudio Data Processing

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The Illumina BeadStudio [15 (link)] output file was processed using the lumi package available in Bioconductor software collection [16 (link)]. The processing included the following steps: quality control of raw data; background subtraction; and variance stabilization using algorithm VST, developed for Illumina data. Values after this processing step should be treated as log-transformed.
Quantile normalization was performed. First, pairwise correlations of intensities were consistently high (>0.95) for the samples. Additionally, we excluded all probes that had detection p-value > 0.05 in all 3 samples. A total of 4 columns (samples) and 11,073 rows (probes) corresponded to 9659 non-redundant genes. Fold changes in gene expression relative to the expression in the control sample were calculated.
Grigorieva O., Arbatskiy M., Novoseletskaya E., Dyachkova U., Ishkin A., Kalinina N, & Efimenko A. (2021). Platelet-Derived Growth Factor Induces SASP-Associated Gene Expression in Human Multipotent Mesenchymal Stromal Cells but Does Not Promote Cell Senescence. Biomedicines, 9(10), 1290.
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10

Microarray Analysis of Differentially Expressed Genes

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Total RNA was extracted as described above. A total of 750 μg of total RNA was reverse-transcribed, converted to cRNA, labeled, purified, and applied onto the human HT-12 v4 BeadChip kit according to the manufacturer’s instructions. First, the respective backgrounds were subtracted from all raw data using Bead Studio (Illumina, Singapore) and then normalized using the cross-correlation method. Subsequently, normalized data were processed for the identification of differentially expressed genes using log2 1.5-fold as the critical value for the mean of log2 n-fold changes in expression between 7DP samples and NCDP controls.
Genes that were differentially expressed two days after the transfection of 7DP were subjected to gene ontology (GO) analysis. The percentage of these genes classified into each GO process was compared with that of the whole genome. Statistically significant (p < 0.05) classes were selected. For the clustering of genes differentially expressed two days post transfection, normalized and log2-transformed data were subtracted from the mean values across all arrays. Hierarchical clustering was then performed for these processed data using average linkages.
Adusumilli L., Facchinello N., Teh C., Busolin G., Le M.T., Yang H., Beffagna G., Campanaro S., Tam W.L., Argenton F., Lim B., Korzh V, & Tiso N. (2020). miR-7 Controls the Dopaminergic/Oligodendroglial Fate through Wnt/β-catenin Signaling Regulation. Cells, 9(3), 711.
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