Image data were analyzed using BeadStudio 2.0 (Illumina, USA). Loci on autosomes were retained, but those in any sample with P > 0.01 were excluded. Data were processed by color balance adjustment, background level correction, and quantile normalization. After additional filtering steps, the methylation levels in the remaining probes were additionally normalized.
Beadstudio 2
Manufactured by Illumina
Sourced in United States
BeadStudio 2.0 is a software application developed by Illumina for the analysis and visualization of data generated from Illumina's microarray platforms. It provides tools for data management, quality control, and basic analysis of gene expression, genotyping, and copy number variation data.
Automatically generated - may contain errors
4 protocols using beadstudio 2
1
Illumina Methylation Data Analysis
2
Illumina Genotyping Quality Control
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Genotyping was performed using Illumina GoldenGate assays on a BeadStation 500G Genotyping System (Illumina, Inc., San Diego, CA, USA). DNA samples (250 ng) were genotyped according to the Illumina protocol. DNA samples from cases and controls were randomly sorted, including 96 duplicated DNA samples for genotyping quality control. Genotype calls were made using the Genotyping module of the BeadStudio 2.0 software (Illumina, Inc.). All genotype data were examined for cluster separation using Illumina quality scores generated by the software. Poorly performing SNPs were excluded, designated by a GenTrain score <0.4 or a cluster separation score <0.6. SNPs were further excluded from controls not in Hardy–Weinberg equilibrium (HWE). As a genotyping quality control, four SNPs were genotyped in duplicate (100 samples) by DNA sequencing.
3
Identifying miR-1290 Target Genes in IAV
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TargetScan was used to predict miR-1290 target genes, as described in previous research.55 As mRNA destabilization is one of the effects that miRNA can exert on target genes, the IAV-downregulated host transcriptome was analyzed using the HumanHT-12 v4 Expression BeadChip Kit (Illumina, San Diego, CA, USA), as described in previous research.56 (link) The data were normalized, and calculation of the false discovery rate (FDR) was performed with Beadstudio 2.0 software (Illumina), using a customized algorithm. The genes that crossed the threshold of detection with p value ≤ 0.05, and which had a differential score p value ≤ 0.05, were considered to be differentially expressed. In addition, 948 host genes derived from RNAi-based screening assays have already been reported in the literature to be important for IAV replication.22 (link), 23 (link), 35 (link), 57 (link), 58 (link), 59 (link), 60 (link) Based on the integration of TargetScan predictions, IAV-downregulated transcriptome analysis results, and literature searches, 62 potential target genes were identified (Table S1 ). Among these, genes that were reported as part of the IAV vRNP interactome,3 (link), 34 (link), 61 (link), 62 (link), 63 (link) and for which antibodies were available in our laboratory, were subsequently selected for further study.
4
Genome-wide SNP Genotyping and CNV Analysis
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Genome-wide SNP genotyping was performed using the Illumina HumanOmni1-Quad v.1.0 BeadChip (Illumina) according to manufactures instructions. To identify putative CNVs, the genotyped single nucleotide polymorphism (SNP) dataset of each sample was analyzed with the QuantiSNP algorithm v.2.2 using log2 R ratio (LRR) values and the B-allele frequency (BAF) values to generate CNV calls. Using Illumina’s Genome Studio software image intensities were extracted and intensity files were processed by using Genome Studio GT module 1.1.9. Each SNP is analyzed independently to cluster and identify genotypes.
Chromosomal aberrations were detected by making comparison of the normalized intensity of a GC sample to a reference samples. Genomic profiles were produced by using the Illumina Genome Viewer (IGV) and Chromosome Browser (ICV) of Illumina's BeadStudio2.0 software, to identify and annotate chromosomal alterations from SNP genotyping data.
Chromosomal aberrations were detected by making comparison of the normalized intensity of a GC sample to a reference samples. Genomic profiles were produced by using the Illumina Genome Viewer (IGV) and Chromosome Browser (ICV) of Illumina's BeadStudio2.0 software, to identify and annotate chromosomal alterations from SNP genotyping data.
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