For chromosomal array comparative genomic hybridization (CGH), DNA of SCC13 cells (P and 10GT) were isolated from exponential cultures using the Qiagen DNEasy Kit. Whole-genome analysis of the cells was conducted using a commercial 60-k oligonucleotide human array-CGH (AMADID 21924, Agilent Technologies, Santa Clara, CA, USA) following the manufacturer's protocol [56 (link)]. Healthy female DNA (Promega Biotech, Madison, WI, USA) was used as hybridization control. Microarray data were extracted and visualized using Feature Extraction software, v10.7 and Agilent Genomic Workbench, v5.0 (Agilent Technologies). Copy-number-altered regions were detected using ADM-2 (set as 6) statistic provided by DNA Analytics, with a minimum number of five consecutive probes. Microarray raw data tables have been deposited in the Gene Expression Omnibus under the accession number GSE180325 . For the subsequent data treatment of the array, different databases were used such as NCBI, Reactome and Uniprot.
Agilent genomic workbench v5
Manufactured by Agilent Technologies
Agilent Genomic Workbench v5.0 is a software application designed for the analysis and visualization of genomic data. It provides a comprehensive suite of tools for tasks such as sequence alignment, variant calling, and data interpretation. The software is intended to facilitate the analysis of genomic information generated by various experimental techniques.
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Lab products found in correlation
Feature extraction software v10, by Agilent Technologies (1 mentions)
Dneasy kit, by Qiagen (1 mentions)
Sureprint g3 human cgh microarray 8 60k, by Agilent Technologies (1 mentions)
Agilent microarray scanner, by Agilent Technologies (1 mentions)
Feature extraction v10, by Agilent Technologies (1 mentions)
Sureprint g3 human cgh microarray 8x60k, by Agilent Technologies (1 mentions)
Earray tool, by Agilent Technologies (1 mentions)
5 protocols using agilent genomic workbench v5
1
Chromosomal Array CGH Analysis
2
Array Comparative Genomic Hybridization Protocol
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Sample preparation, slide hybridization, and analysis were performed using SurePrint G3 Human CGH Microarray 8×60K (Agilent, Santa Clara, CA) according to the manufacturer’s instructions. Sex-matched commercial DNA samples (Promega) were used as reference DNA during aCGH. The arrays were scanned at 2-mm resolution using Agilent microarray scanner and analyzed using Feature Extraction v10.7 and Agilent Genomic Workbench v5.0 softwares. The Aberration Detection Method 2 (ADM2) algorithm prompted by Genomic Workbench software was used to compute and assist the identification of aberrations for a given sample (threshold = 5; log2 ratio = 0.3). To calculate the estimated percentage of mosaicism we used the formula determined by Cheung et al. [26 (link)].
3
Genomic Analysis of Murine Lymphoma
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Genomic DNA was extracted from CD19+ cells isolated from transgenic (n=19) and WT spleens (n=2, used as normal hybridization controls). Whole-genome analysis was conducted using a 180-K oligonucleotide mouse aCGH microchip (AMADID 27411, Agilent Technologies), following standard protocols52 (link). Microarray data were extracted and visualized using Feature Extraction v10.7 and Agilent Genomic Workbench v5.0 softwares (Agilent Technologies). Regions with DNA copy number abnormalities were detected using ADM-2 (seta s 6) statistic provided by DNA Analytics, with a minimum number of 5 consecutive probes. Genomic build mm7 was used for the experiment. For comparison of the murine lymphoma genomic changes with those present in human disease, two previously published studies including the aCGH analysis of 136 samples from patients with SMZL were used35 (link)36 (link).
4
CGH Microarray Genomic Analysis
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Genomic DNA extraction, sample preparation, slide hybridization and analysis were performed using SurePrint G3 Human CGH Microarray 8x60K (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer’s recommendations. The arrays were scanned at 2-μm resolution and analyzed using Feature Extraction v10.7 and Agilent Genomic Workbench v5.0 software (Agilent Technologies), as previously reported [9 (link)].
5
Comprehensive Genomic Profiling by a-CGH
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Detection of gene copy number was performed by array-Comparative Genomic Hybridization (a-CGH) experiments. Whole genome analysis was conducted using a human whole genome 400k array (SurePrint G3 Human CGH microarray 2x400, AMADID 021850, Agilent Technologies, Santa Clara, CA), following standard and manufacturer’s protocol [27 (link)]. For the analysis of the region chr20:47897125–62435965, the array was designed using Agilent’s e-array tool (Agilent Technologies) following the manufacturer’s instruction (https://earray.chem.agilent.com/ ). In both cases, healthy male and female donor samples were used as hybridization controls.
Microarray data were extracted and visualized using Feature Extraction software v10.7 and Agilent Genomic Workbench v5.0 (Agilent Technologies). Copy number altered regions were analyzed using ADAM-2 (set as 6) statistic provided by DNA Analytics, with a minimum number of 5 consecutive probes (the analysis resolution, thus, is approximately 25 kb for most of the regions for the whole genome array and 400 bp for the custom array). Genomic build hg19 was used for the experiments.
Microarray data were extracted and visualized using Feature Extraction software v10.7 and Agilent Genomic Workbench v5.0 (Agilent Technologies). Copy number altered regions were analyzed using ADAM-2 (set as 6) statistic provided by DNA Analytics, with a minimum number of 5 consecutive probes (the analysis resolution, thus, is approximately 25 kb for most of the regions for the whole genome array and 400 bp for the custom array). Genomic build hg19 was used for the experiments.
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