Agilent genomic workbench software v7

Manufactured by Agilent Technologies

Agilent Genomic Workbench software v7.0 is a comprehensive bioinformatics platform designed for the analysis and interpretation of genomic data. The software provides a suite of tools for tasks such as sequence alignment, variant calling, and data visualization. It is compatible with a range of input file formats and enables users to perform complex genomic analyses within a user-friendly interface.

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Lab products found in correlation

Qiaamp dna micro kit, by Qiagen (3 mentions) Genomic dna high throughput uls labeling kit, by Agilent Technologies (2 mentions) Sureprint g3 human cgh microarray 4 180k, by Agilent Technologies (2 mentions) Cytogenomics software, by Agilent Technologies (2 mentions) Agilent dna microarray scanner g2565ca, by Agilent Technologies (1 mentions) Human reference dna, by Agilent Technologies (1 mentions) Kreapure columns, by Agilent Technologies (1 mentions) Genomic dna and human reference dna, by Promega (1 mentions)

Close spelling variants of this product

Genomic Workbench software v7.0.4.0 Genomic Workbench v7.0 Agilent Genomic Workbench Genomic Workbench software Agilent Workbench Software

4 protocols using agilent genomic workbench software v7

FFPE Tissue DNA Profiling Using CGH

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Genomic DNA was extracted from FFPE tissue using a QIAamp, DNA micro kit (Qiagen, Hilden, Germany). Genomic DNA and human reference DNA (Promega) were labeled with cyanine 5 (Cy5) and cyanine 3 (Cy3), respectively, using the Genomic DNA High-Throughput ULS Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and co-hybridized onto a Sureprint G3 Human CGH microarray 4×180K (Agilent Technologies) following manufacturer’s recommendations. Data were analysed using Agilent Genomic Workbench software v7.0, or by Cytogenomics software (v2.9.2.4, Agilent), and expressed according to the human reference genome hg19 (GRCh37, Genome Reference Consortium Human Reference 37). The identification of aberrant copy number segments was based on ADM-2 segmentation algorithm with a threshold of 6.0.

Alholle A., Karanian M., Brini A.T., Morris M.R., Kannappan V., Niada S., Niblett A., Ranchère-Vince D., Pissaloux D., Delfour C., Gonzalez A.M., Antonescu C.R., Sumathi V., Tirode F, & Latif F. (2018). Genetic analyses of undifferentiated small round cell sarcoma identifies a novel sarcoma subtype with a recurrent CRTC1-SS18 gene fusion. The Journal of pathology, 245(2), 186-196.

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Agilent SurePrint G3 Human CGH Microarray

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CGH was performed using the Agilent SurePrint G3 Human CGH 60 K microarray (Agilent Technologies) by spanning the entire human genome at a median resolution of 41 kb. For the hybridization, 500 ng of genomic DNA from the test samples and human reference DNA (Agilent Technologies) were differentially labeled with Cy5–2′-deoxycytidine 5′-triphosphate (dCTP) and Cy3-dCTP by random priming. An Agilent DNA Microarray scanner G2565CA (Agilent Technologies) was used to scan the arrays, and data were extracted and visualized using Feature Extraction software v10.7. Copy number–altered regions were detected with Agilent Genomic Workbench software v7.0 (Agilent Technologies) using the Aberration Detection Method 2 algorithm set as 6, with a minimum number of three consecutive probes.

Villarroya-Beltri C., Osorio A., Torres-Ruiz R., Gómez-Sánchez D., Trakala M., Sánchez-Belmonte A., Mercadillo F., Hurtado B., Pitarch B., Hernández-Núñez A., Gómez-Caturla A., Rueda D., Perea J., Rodríguez-Perales S., Malumbres M, & Urioste M. (2022). Biallelic germline mutations in MAD1L1 induce a syndrome of aneuploidy with high tumor susceptibility. Science Advances, 8(44), eabq5914.

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Genomic DNA Extraction and Microarray Analysis

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DNA extraction was performed by macrodissecting FFPE tumor blocks followed by the use of the QIAamp DNA micro kit (Qiagen #56304, Hilden, De). Fragmentation and labeling were carried out according to the manufacturer's protocol (Agilent Technologies), using 1.5 µg of genomic DNA. Tumor DNA was labeled in Cy5, and a reference DNA with male or female sex-mismatch (Promega #G1471 and #G1521, Madison, USA) was labeled in Cy3. The labeled samples were then purified using KREApure columns (Agilent Technologies #5190-0418). The labeling efficiency was calculated using a Nanodrop ND2000 spectrophotometer. Cohybridization was performed on the 4 × 180K Agilent SurePrint G3 Human whole-genome design (Agilent Technologies # G4449A). The slides were washed, dried and scanned on the Agilent SureScan microarray scanner. The scan images were processed using Agilent Feature Extraction software V11.5 and the analysis was carried out using Agilent Genomic Workbench software V7.0.

de la Fouchardiere A., Tirode F., Castillo C., Buisson A., Boivin F., Macagno N, & Pissaloux D. (2022). Attempting to Solve the Pigmented Epithelioid Melanocytoma (PEM) Conundrum: PRKAR1A Inactivation Can Occur in Different Genetic Backgrounds (Common, Blue, and Spitz Subgroups) With Variation in Their Clinicopathologic Characteristics. The American journal of surgical pathology, 46(8).

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Profiling Genomic Copy Number Variations

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Genomic DNA was extracted from formalin-fixed paraffinembedded tissue using QIAamp, DNA micro kit (Qiagen, Hilden, Germany). Genomic DNA and human reference DNA (Promega) were labeled with cyanin 5 (Cy5) and cyanine 3 (Cy3), respectively, using the Genomic DNA High-Throughput ULS Labeling Kit (Agilent Technologies, Santa Clara, California) and co-hybridized onto a Sureprint G3 Human CGH microarray 4 × 180K (Agilent) following manufacturer's recommendations. Data were analyzed by Agilent Genomic Workbench software v7.0 or by Cytogenomics software (v2.9.2.4, Agilent) and expressed according to the human reference hg19 (GRCh37, Genome Reference Consortium Human Reference 36). The identification of aberrant copy number segments was based on ADM-2 segmentation algorithm with a threshold of 6.0.

Dadone-Montaudié B., Alberti L., Duc A., Delespaul L., Delespaul L., Lesluyes T., Pérot G., Lançon A., Paindavoine S., Di Mauro I., Blay J.Y., de la Fouchardière A., Chibon F., Karanian M., MacGrogan G., Kubiniek V., Keslair F., Cardot-Leccia N., Michot A., Perrin V., Zekri Y., Coindre J.M., Tirode F., Pedeutour F., Ranchère-Vince D., Le Loarer F, & Pissaloux D. (2018). Alternative PDGFD rearrangements in dermatofibrosarcomas protuberans without PDGFB fusions. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 31(11).

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