DNA was available from 40 of the 44 samples and was extracted from BM (n = 33) or peripheral blood (n = 7); in 27/40 (68%) cases, a remission sample could be included as a control. The HumanOmni1-Quad BeadChip, containing >1 million markers with a median marker spacing of 1.5 kb (Illumina, San Diego, CA, USA), was used. The analyses were performed according to the manufacturer’s instructions, and data analysis was done using the GenomeStudio software 2011.1 (Illumina), extracting probe positions from the GRCh37 genome build (http://www.ensembl.org/Homo_sapiens/Info/Index ). Imbalances seen in remission samples or overlapping with copy number polymorphisms listed in the Database of Genomic Variants (http://projects.tcag.ca/variation/ ) were excluded from further analysis, and so were deletions involving the TCR and immunoglobulin loci because they most likely represent somatic rearrangements clonotypic for the malignant lymphoid cells rather than oncogenic events [47 (link)].
Genomestudio software 2011
Manufactured by Illumina
Sourced in China
GenomeStudio software 2011.1 is a data analysis software designed for use with Illumina's microarray and sequencing platforms. It provides a comprehensive suite of tools for visualizing and analyzing genomic data generated by Illumina's technology.
Automatically generated - may contain errors
Lab products found in correlation
Ez dna methylation kit, by Zymo Research (2 mentions)
Humanomni1 quad beadchip, by Illumina (1 mentions)
Wizard genomic dna purification kit, by Promega (1 mentions)
Infinium methylationepic beadchip, by Illumina (1 mentions)
Infinium human methylationepic beadchip, by Illumina (1 mentions)
Iscan sq scanner, by Illumina (1 mentions)
Genelute mammalian total rna miniprep kit, by Merck Group (1 mentions)
Humanht 12 v4 expression beadchip, by Illumina (1 mentions)
Hiscan 2000, by Illumina (1 mentions)
Dneasy blood and tissue kit, by Zymo Research (1 mentions)
Infinium humanmethylation450 beadchip, by Illumina (1 mentions)
Mousewg 6 v2.0 expression beadchip, by Illumina (1 mentions)
Infinium humanmethylation450 beadchip array, by Illumina (1 mentions)
Ez 96 dna methylation kit, by Zymo Research (1 mentions)
10 protocols using genomestudio software 2011
1
Genome-wide Copy Number Profiling
2
Genome-wide DNA Methylation Analysis of Cancer Cells
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Genome-wide DNA methylation analysis of over 850,000 methylation sites was performed using the Infinium MethylationEPIC BeadChip (Illumina) in RPMI7951, C32, Malme-3M, SK-MEL-28, EPZ-6438-treated C32, and azacytidine-treated Malme-3M cells. 5 × 105 C32 and Malme-3M cells were treated with 50 µM EPZ-6438 and azacytidine respectively in 6-well flat-bottom plates containing 3 ml of culture medium for 72 h. Cells were collected, genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega) and was sodium bisulfite treated using the EZ DNA Methylation Kit (Zymo Research) according to instructions from manufacturers. DNA methylation levels were analyzed by GenomeStudio Software 2011.1 (Illumina). Methylation data are available in the Gene Expression Omnibus (GEO) database (accession number GSE143614 ).
3
Genome-Wide SNP Analysis of Atlantic Cod Population
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Genotypes were clustered using the Illumina GenomeStudio software 2011.1, and 9,187 SNPs were found to be actual polymorphic loci called for at least 95% of individuals across the 378 samples. All 9,187 SNPs are identified in supplementary table S1 , Supplementary Material online, by their accession number in the dbSNP database (Sherry et al. 2001 (link)).
The R software 3.1.3 (R Core Team 2014 ) was used for subsequent analyses. The GenABEL R package (Aulchenko et al. 2007 (link)) was applied to test for deviations from Hardy–Weinberg equilibrium across, while minor-allele frequency and average observed heterozygocity was estimated with the hierfstat R package (Goudet 2005 ). LD was estimated as composite LD (Schaid 2004 (link)), a method suitable for unphased genotype data, for all pairs of SNPs with the R software utilizing the algorithm proposed by Gao et al. (2009). SNP pairs with LD >0.5 were classified as being in high LD, and physical extent of LD blocks was estimated by summing the lengths of the scaffolds in the Atlantic cod genome assembly (Star et al. 2011 (link)) anchoring SNPs spanned by the blocks.
The R software 3.1.3 (R Core Team 2014 ) was used for subsequent analyses. The GenABEL R package (Aulchenko et al. 2007 (link)) was applied to test for deviations from Hardy–Weinberg equilibrium across, while minor-allele frequency and average observed heterozygocity was estimated with the hierfstat R package (Goudet 2005 ). LD was estimated as composite LD (Schaid 2004 (link)), a method suitable for unphased genotype data, for all pairs of SNPs with the R software utilizing the algorithm proposed by Gao et al. (2009). SNP pairs with LD >0.5 were classified as being in high LD, and physical extent of LD blocks was estimated by summing the lengths of the scaffolds in the Atlantic cod genome assembly (Star et al. 2011 (link)) anchoring SNPs spanned by the blocks.
4
Genome-Wide DNA Methylation Analysis
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DNA methylation assessment was performed using the Infinium Human MethylationEPIC Bead-Chip (Illumina Inc.) to interrogate more than 850,000 CpG positions across the genome. The raw image intensities of the hybridized arrays were scanned using an iScan SQ scanner (Illumina). The obtained raw data were processed and standardized using GenomeStudio software 2011.1 (Illumina), and the background method was chosen as the normalization method. Methylation values were estimated as β-values that range between 0 (completely unmethylated) and 1 (completely methylated). The experimental process and technical validation were performed according to the manufacturer's instructions.
5
Zanubrutinib Transcriptomics in Prostate Cancer
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Tumor RNA was extracted from the mice used in the C4-2 zanubrutinib treatment experiment, 4 samples from each group. RNA was extracted with GenElute Mammalian Total RNA miniprep kit (Sigma-Aldrich). The Case Western Reserve University Genomics Core performed the RNA-Seq using the HumanHT-12 v4 Expression BeadChip and iScan (Illumina). Hybrid signals were analyzed with Illumina GenomeStudio Software 2011.1 and normalized to the vehicle control group. Heatmaps were generated with HemI software (version 1.0). GSEA was used to correlate the 5α-Abi expression data with an androgen receptor-selective gene set described elsewhere (53 (link)). The GSEA enrichment plot was generated as described elsewhere (54 (link)).
6
Genome-wide DNA Methylation Analysis
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Combined placental DNA from the 30 placental DNAm samples described in Table 2 was purified using the Qiagen DNeasy Blood and Tissue kit, and 750 ng of this DNA was bisulfite converted using the EZ DNA Methylation kit (Zymo Research) following the manufacturer’s protocols. Samples were processed following the Illumina Infinium HumanMethylation450 BeadChip (450k array) protocol [72 ] and scanned using the Illumina HiScan 2000. Raw intensity was read into Illumina Genome Studio software 2011.1, and background normalization was applied. Data processing was performed as described in Price et al. [73 ], including sample quality checks, probe filtering, data normalization, and batch correction. This processing pipeline resulted in a final N = 442,355 cytosine-guanine dinucleotide (CpG) sites from the 450k array for analysis.
7
Adenovirus-Mediated Overexpression of ATF4 in HL-1 Cells
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HL-1 cells were infected with Adenovirus containing a GFP, ATF4wt, or ATF4ΔRK construct. After 48 h, cells were rapidly paced for 20 h. Biotin-labeled cRNA was hybridized on Illumina MouseWG-6 v2.0 expression BeadChips. In the Illumina GenomeStudio Software 2011.1, raw data were normalized using the quantile algorithm. Differential gene expression was assessed on the basis of grouped replicates and thresholds for expression ratios or, alternatively, for both expression ratios and statistical significance employing the t-test model, based on standard deviations between biological replicates. Filtering of genes was performed using sorting and autofiltering functions in MS Excel (p value ≤ 0.05). Functional annotation analysis was carried out using DAVID 6.7.
8
DNA Methylation Analysis of Spinal Cord
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DNA was extracted from the spinal cord using a DNA extraction kit (TIANamp Genomic DNA Kit, China) according to the manufacturer’s instructions. Five hundred nanograms of bisulfite-converted DNA per sample were analyzed by Illumina Infinium Human Methylation 450 BeadChip array (Illumina, China). Raw data analysis and preliminary data quality control were performed with GenomeStudio software 2011.1 (Illumina, China). Specific experimental procedures for DNA methylation sequencing are shown in Figure 1 . For further gene expression analysis, all data were imported into Cytoscape software (v3.6.1) and GraphPad Prism software (Graph Pad v6.01) for functional analysis and statistical analysis [24 (link)]. Differentially methylated genes (DMGs) were identified (mean methylation difference ≥20, P<0.001) as described earlier [25 ]. Using the bioinformatics resources of DAVID 6.7 (https://david.ncifcrf.gov/ ), the Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially methylated genes were performed [26 (link)].
9
Genome-wide DNA Methylation Analysis
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The Infinium MethylationEPIC BeadChip assay, a genome-wide DNA methylation analysis technique has been performed with C4-2 and DKD cells. This array-based assay uses bisulfite converted DNA and Illumina® technology to quantitatively detect the CpG island methylation level throughout the genome at a resolution of single nucleotide bases.
Deamination of DNA is performed with the EZ-96 DNA Methylation Kit (Zymo Research) according to Illumina’s guidelines.. Array Scan Infinium Control BeadChips have been used which are equipped with a set of internal control probes. These control probes are used for identification of test samples with different data characteristics based on threshold parameters. These controls are also evaluated as per relative intensities. are The EPIC Array analysis has been done with GenomeStudio® Software 2011.1, Methylation Module v1.9 following the Illumina Methylation Module user guidelines (Controls Dashboard).
Deamination of DNA is performed with the EZ-96 DNA Methylation Kit (Zymo Research) according to Illumina’s guidelines.. Array Scan Infinium Control BeadChips have been used which are equipped with a set of internal control probes. These control probes are used for identification of test samples with different data characteristics based on threshold parameters. These controls are also evaluated as per relative intensities. are The EPIC Array analysis has been done with GenomeStudio® Software 2011.1, Methylation Module v1.9 following the Illumina Methylation Module user guidelines (Controls Dashboard).
10
Genotyping from Bloodspots and Saliva
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For the cases, genomic DNA was extracted from bloodspots78 (link) and genotyped using the HumanOmni2.5-4 v1 BeadChip (Illumina, San Diego, CA), as previously described56 (link). For the controls, saliva was collected and genotyped by the NIH Center for Inherited Disease Research using the same Human Omni2.5-4 v1 BeadChip methodology, as previously described.
We merged raw intensities data (*.idat) files of cases and controls and carried out joint calling, to reduce batch effects. Clustering and genotyping were performed using GenomeStudio software 2011.1 (Illumina, 2011). Quality control procedures were performed, including filtering by call rate, mismatch between observed and reported gender and possible gender abnormalities as described in Wang et al.56 (link), and tri-allelic and ambiguous (AT/CG) SNPs were removed. Overall, a total of 2,015,750 SNPs were used in our downstream analyses.
We merged raw intensities data (*.idat) files of cases and controls and carried out joint calling, to reduce batch effects. Clustering and genotyping were performed using GenomeStudio software 2011.1 (Illumina, 2011). Quality control procedures were performed, including filtering by call rate, mismatch between observed and reported gender and possible gender abnormalities as described in Wang et al.56 (link), and tri-allelic and ambiguous (AT/CG) SNPs were removed. Overall, a total of 2,015,750 SNPs were used in our downstream analyses.
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