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104 results for “Infinium”
High density SNP genotypes (Infinium Human CytoSNP-850K v1.2 BeadChip) of ERAP2-WT and ERAP2-KO Birdshot LCL
<p>SNP genotype data was performed on DNA isolated from WT and CRISPR-Cas9 edited LCLs (ERAP2-KO) according to standard procedures using the Infinium Human CytoSNP-850K v1.2 BeadChip (Illumina, San Diego, CA, USA). SNP-array results and data analysis were carried out using NxClinical software v5.1 (BioDiscovery, Los Angeles, CA, USA). Human genome build Feb. 2009 GRCh37/hg19 was used. </p>
The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip, supplementary table 3
<p>Supplementary table 3: Summary statistics from an EWAS assessing the relationship between variance in DNA methylation value and DNA input level.</p>
Determining haploblocks and haplotypes in the MAGIC winter wheat population WM-800 based on the wheat 15k Infinium and the 135k Affymetrix SNP arrays
<p><span>Haplotypes are derived from single nucleotide polymorphisms (SNPs). They are beneficial (i) to remove redundant sequence information in genetic populations and, more important, (ii) to distinguish more than two variants/alleles at a genomic locus. A haploblock locus, made of multiple haplotypes, is very useful in multiparent-advanced-generation-intercross (MAGIC) populations, where, ideally, multiple founder alleles need to be distinguished at each locus to subsequently carry out efficient genome-wide association analysis studies (GWAS). </span></p> <p><span>In this regard, the dataset contains genotype matrices (made of SNP, haploblock and haplotype data) for 800 lines of the MAGIC WHEAT population WM-800 (Sannemann et al. 2018). The datasets are based on genotyping the lines with both the already published wheat 15k Infinium SNP array (Sannemann et al. 2018) and the new wheat 135k Affymetrix SNP array.</span></p>
A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data
<p><strong>Background </strong></p> <p>The Infinium EPIC array measures the methylation status of > 850,000 CpG sites. The EPIC BeadChip uses a two-array design: Infinium Type I and Type II probes. These probe types exhibit different technical characteristics which may confound analyses. Numerous normalization and pre-processing methods have been developed to reduce probe type bias as well as other issues such as background and dye bias. <strong> </strong></p> <p><strong>Methods</strong></p> <p>This study evaluates the performance of various normalization methods using 16 replicated samples and three metrics: absolute beta-value difference, overlap of non-replicated CpGs between replicate pairs, and effect on beta-value distributions. Additionally, we carried out Pearson's correlation and intraclass correlation coefficient (ICC) analyses using both raw and SeSAMe 2 normalized data. <strong> </strong></p> <p><strong>Results</strong></p> <p>The method we define as SeSAMe 2, which consists of the application of the regular SeSAMe pipeline with an additional round of QC, pOOBAH masking, was found to be the best-performing normalization method, while quantile-based methods were found to be the worst performing methods. Whole-array Pearson's correlations were found to be high. However, in agreement with previous studies, a substantial proportion of the probes on the EPIC array showed poor reproducibility (ICC < 0.50). The majority of poor-performing probes have beta values close to either 0 or 1, and relatively low standard deviations. These results suggest that probe reliability is largely the result of limited biological variation rather than technical measurement variation. Importantly, normalizing the data with SeSAMe 2 dramatically improved ICC estimates, with the proportion of probes with ICC values > 0.50 increasing from 45.18% (raw data) to 61.35% (SeSAMe 2).</p>
A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data
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Determining haploblocks and haplotypes in the MAGIC winter wheat population WM-800 based on the wheat 15k Infinium and the 135k Affymetrix SNP arrays
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Data from: New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array
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Data from: Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip
Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.
Data from: Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip
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Methylation data from nine tissues from GTEx samples profiled with Infinium HumanMethylationEPIC BeadChip
GEO Series GSE213478. Homo sapiens. 987 samples. Type: Methylation profiling by array.
DNA methylation analysis of ovarian cancers and normal peripheral blood lymphocyte DNA by Illumina Infinium platform
GEO Series GSE26989. Homo sapiens. 53 samples. Type: Methylation profiling by array.
Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. (Infinium Methylation450K)
GEO Series GSE217732. Homo sapiens. 19 samples. Type: Methylation profiling by genome tiling array.
Genotyping analysis employing Illumina Infinium ImmunoArray-24 v2.0 BeadChip
GEO Series GSE105120. Homo sapiens. 170 samples. Type: Genome variation profiling by SNP array.
Illumina Infinium MethylationEPIC BeadChip (850k) data of germ cell tumor-related somatic-type maligancies
GEO Series GSE219033. Homo sapiens. 20 samples. Type: Methylation profiling by array.
Multi-omics data analysis for the JGOG3025-TR2 ovarian cancer cohort [Infinium MethylationEPIC]
GEO Series GSE263434. Homo sapiens. 285 samples. Type: Methylation profiling by genome tiling array.
Evaluating The Infinium Human MethylationEPIC v2 BeadChip
GEO Series GSE228820. Homo sapiens. 56 samples. Type: Methylation profiling by genome tiling array.
Optimizing the experimental and computational methods for Infinium DNA methylation BeadChip on low input and single cells
GEO Series GSE239290. Mus musculus. 146 samples. Type: Methylation profiling by genome tiling array.
Wide methylation analysis in vestibular schwannoma [Infinium HumanMethylation450 BeadChip]
GEO Series GSE56596. Homo sapiens. 45 samples. Type: Methylation profiling by genome tiling array.
Illumina Infinium HumanMethylation450 data for human whole blood samples and for mixtures of purified white blood cells reconstructing human blood
GEO Series GSE54670. Homo sapiens. 12 samples. Type: Methylation profiling by array.
MiR-1253 exerts tumor-suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3) (Infinium MethylationEPIC dataset)
GEO Series GSE148388. Homo sapiens. 56 samples. Type: Methylation profiling by genome tiling array.
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