The screening of genomic rearrangements and mapping of the breakpoints were performed with the HumanCytoSNP-12 BeadChip platform (Illumina), comprising 301,232 SNPs. Genomic DNA was prepared from peripheral blood and then extracted using a DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer’s protocol. Genomic DNA samples were adjusted to a final concentration 50 ng/μL. DNA amplification, tagging and hybridization were performed according to the manufacturer's protocol. Array slides were scanned on the iScan Reader (Illumina). The GenomeStudio V2011 software (Illumina) was used to analyse the genotypes (human genome build 37/Hg19 for analysis) and evaluate the experimental quality. The call rates of the samples were greater than 99.5%.
Genomestudio v2011
Manufactured by Illumina
Sourced in United States
GenomeStudio v2011.1 is a data analysis software developed by Illumina for processing and analyzing data generated from Illumina's microarray platforms. The software provides a suite of tools for data visualization, quality control, and downstream analysis.
Automatically generated - may contain errors
Lab products found in correlation
Amersham fluorolink streptavidin cy3, by GE Healthcare (8 mentions)
Iscan system, by Illumina (7 mentions)
Dneasy 96 plant kit, by Qiagen (6 mentions)
Bead array reader confocal scanner, by Illumina (6 mentions)
Nanodrop spectrophotometer, by Thermo Fisher Scientific (6 mentions)
Beadarray reader, by Illumina (6 mentions)
Ez dna methylation kit, by Zymo Research (6 mentions)
Nanodrop 1000 spectrophotometer, by Thermo Fisher Scientific (5 mentions)
Iscan reader, by Illumina (4 mentions)
Dneasy blood tissue kit, by Qiagen (4 mentions)
Humanht 12 v4 expression beadchip, by Illumina (4 mentions)
Trizol reagent, by Thermo Fisher Scientific (4 mentions)
Rneasy mini kit, by Qiagen (3 mentions)
Genotyping module v 1.9.4, by Illumina (3 mentions)
Infinium genotyping data analysis technical note, by Illumina (3 mentions)
Trizol, by Thermo Fisher Scientific (3 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions)
Infinium cytosnp 850 k beadchips, by Illumina (3 mentions)
Qubit dsdna br assay kit, by Thermo Fisher Scientific (3 mentions)
Nucleospin tissue kit, by Macherey-Nagel (3 mentions)
198 protocols using genomestudio v2011
1
Genome-wide SNP Genotyping for Structural Variations
2
Pediatric Glioma Expression and Methylation
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The gene expression profile data GSE50021 was downloaded from the Gene Expression Omnibus database (GEO, http://www.ncbi.nlm.nih.gov/geo/ ) (15 (link)). Gene expression profiling was based on the GPL13938 platform using the Illumina HumanHT-12 WG-DASL V4.0 expression BeadChip (Illumina Inc., San Diego, CA, USA). The array consists of 29,377 probe-sets, which it is possible to use to detect the transcription level of 20,817 human genes. A total of 45 samples, including 10 specimens of normal brain tissues and 35 specimens of glioma tissues from children with a mean age of 1.008±1.910 years were available for the expression array.
The dual channel methylation microarray data GSE50022, was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/ ) (15 (link)). Gene expression profiling was based on the platform of GPL16304 using the Illumina HumanMethylation450 BeadChip (UBC enhanced annotation v1.0; Illumina, Inc.). The array consisted of 485,512 probe-sets, which detect >485,000 methylation sites per sample at single-nucleotide resolution. Methylation data of 28 samples from patients with glioma (mean age, 0.943±0.782 years) were analyzed in the present study. The methylation index matrix was processed with GenomeStudio v2011 software (Illumina, Inc.) which indicated the methylation ratios of the probes.
The dual channel methylation microarray data GSE50022, was downloaded from the GEO database (
3
Genome-Wide Genotyping of Twin Cohort
4
Bovine SNP50 v2 Genotyping Protocol
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The animals were investigated for their NCAPG I442M (rs109570900) and GDF Q204X (rs110344317) genotypes as described by Weikard et al. [8 (link)]. For further GWAS and network analyses, a subset of 176 animals was genotyped with Illumina Bovine SNP50 v2 (50k) chips, which were processed according to Illumina Infinium HD Assay Ultra guidelines and read out on an Illumina iScan system. Quality control with Illumina Genome Studio v2011 was carried out as follows: all SNP clusters with either a call frequency < 0.98, a GenTrain Score < 0.68 or a Chi2-test for deviation from Hardy-Weinberg equilibrium < 0.005 were manually checked and re-clustered if possible. After manual re-clustering, only autosomal SNPs with a call frequency > 0.85 and a minor allele frequency > 0.01 (n = 44,507 SNPs passing filtering) as well as all samples with a call rate > 0.98 were included in further analyses.
5
Illumina HumanCNV370 Genotyping Protocol
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DNA was processed using the Illumina HumanCNV370-Quad/OmniExpress genotyping microarray according to the protocol. Data analysis was performed using the Illumina GenomeStudio v.2011 and Illumina cnvPartition (ver 3.2.0) software program.
6
Illumina Bead Array DNA Methylation Analysis
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The Illumina GenomestudioV2011 program (Illumina Ltd.) was used to analyze BeadArray data to assign site-specific DNA methylation β-values to each CpG site. The Beadchips were subjected to fluorescently labeled nucleotides of two different colors, each corresponding to the cytosine (methylated, M) or uracil (unmethylated, U) identity of the bisulfite- converted nucleotide at a specific CpG site. The proportion of methylation (β) were calculated as: β = Max(M, 0)/[Max(M, 0) + Max(U, 0) + 100]. The methylation status for each probe was calculated as a β- value (ranged 0~1), which representing low to high levels of methylation21 22 (link). After further filtering of overlaps, 386,135 probes were leaving for final analysis. P > 0.05 indicated that the data points were not significantly different from background measurements.
7
Genotyping Brassica F2 Lines with Illumina 60K SNP Array
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The Illumina Infinium Brassica 60K SNP Array (Clarke et al., 2016 (link)) was used for genotyping 190 F2 lines and two parental lines (Supplementary Table 2 ). Total genomic DNA was extracted using DP321-03 DNA extraction kits (Tiangen, Beijing, China). SNP genotyping was performed in the National Key Laboratory of Crop Genetic Improvement, National Subcenter of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China, according to the Infinium HD Assay Ultra manual protocols. Illumina HiSCAN scanner was used for imaging the hybridized chips. GenomeStudio v2011 (Illumina, Inc.) genotyping software was used for allele calling. SNP markers were named using the SNP plus index numbers assigned by GenomeStudio from the chip information (Clarke et al., 2016 (link)), followed by chromosome number. SNP positions were obtained by BLAST search (e ≤ 1e−50) against the B. napus genome reference Darmor v4.1 (Chalhoub et al., 2014 (link)).
8
Bovine Whole Genome Genotyping and CNVR Analysis
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Whole blood was collected from each cow, and genomic DNA was isolated using the Easy-DNA kit (Invitrogen, Cat. #K1800-01). All sample were genotyped using the using the Illumina BovineHD BeadChip Array (Illumina, Cat. #WG-450-1002), which contains 735,293 autosomal SNPs [42 (link)], according to the manufacturer’s instructions. SNP clustering and genotype calling was performed using GenomeStudio V2011 (Illumina, version 1.9.4), and all markers passed quality control (call rate >98%). The UMD3.1 assembly was used to map SNPs position [43 ]. CNVR were detected as previouly reported [9 (link)], detected using PennCNV software (version June 2011) [44 (link), 45 ], which incorporates factors including log R ratio (LRR), B allele frequency (BAF), marker distance, and the population frequency of B allele (PFB) into a hidden Markov model.
9
Genotyping Japanese Black Cows
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Blood was collected from 791 Japanese Black cows. Genomic DNA was extracted using the Easy-DNA kit (Invitrogen, Cat. #K1800–01). All samples were genotyped using the BovineHD BeadChip Array (Illumina, Cat. #WG-450-1002) [41 (link)]. SNPs genotype calling were performed using GenomeStudio V2011 (Illumina, version 1.9.4). The ARS-UCD1.2 assembly was used to map the SNP position [42 ]. CNVR was detected as previously reported [15 (link)], using PennCNV software (version June 2011) [43 (link)].
10
Genotyping HD Patients via Illumina BeadArray
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We have previously designed a genotyping panel of 96 SNPs using a Goldengate assay on the Illumina BeadArray platform [33] (link). Briefly, 96 SNPs were selected for the genotyping assay based on LD patterns from Hapmap, dbSNP and in-house sequencing. DNA samples from the Huntington Disease BioBank at the University of British Columbia from 390 different HD pedigrees were collected. 1151 samples were genotyped using Illumina GenomeStudio v2011 and subsequently phased based on information from family trios using the PHASE 2.0 software.
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