Agilent array scanner

Manufactured by Agilent Technologies

The Agilent Array Scanner is a high-performance microarray scanner designed for the analysis of DNA, RNA, and protein microarrays. It offers precise and accurate scanning capabilities to enable reliable data generation for a variety of applications.

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Agilent scanner (115 citations) Agilent arrays (7 citations) Agilent array scanner G2505C (3 citations) Agilent Gene Array Scanner G2500A (2 citations)

5 protocols using agilent array scanner

Microarray Analysis of Gene Expression

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Microarray analysis was performed as previously described (Pai et al., 2014 (link); Rallis et al., 2013 (link)). Experiments were conducted in duplicate with a dye swap. RNAs from two independent biological replicates have been utilized for cDNA production. Fig. 6C shows average expression ratios from the two repeats. Original data have been deposited in ArrayExpress under accession number E-MTAB-6795. In brief, Alexa Fluor 555- or 647-labelled cDNA was produced from the RNA, using a Superscript direct cDNA labelling system (Invitrogen) and Alexa Fluor 555 and 647 dUTP mix. cDNAs were then purified using an Invitrogen PureLink PCR Purification system and hybridized to the array using a Gene Expression Hybridization kit (Agilent). The arrays are Agilent custom-designed containing 60-mer oligonucleotides synthesized in situ containing 15,000 probes. Following hybridization for at least 17 h, the arrays were washed using a Gene Expression Wash Buffer kit (Agilent) and scanned in an Agilent Array Scanner. Signals were extracted using GenePix software.

Pai C.C., Hsu K.F., Durley S.C., Keszthelyi A., Kearsey S.E., Rallis C., Folkes L.K., Deegan R., Wilkins S.E., Pfister S.X., De León N., Schofield C.J., Bähler J., Carr A.M, & Humphrey T.C. (2019). An essential role for dNTP homeostasis following CDK-induced replication stress. Journal of Cell Science, 132(6), jcs226969.

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Array-CGH Analysis of Genomic Copy Number

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Genomic DNA was isolated from SUM44 and LCCTam cells, the latter cultured in the absence of 4HT for 14 days, using the illustra triplePrep kit (GE Healthcare, Buckinghamshire, UK) according to manufacturer’s instructions. DNA copy number analysis was performed using an oligonucleotide array-CGH platform (SurePrint G3 Human CGH Microarray 8×60K; Agilent Technologies Inc., Santa Clara, CA), as published previously (Torresan, et al. 2014 (link)). DNA isolated from peripheral blood from multiple normal individuals was used as reference DNA. Briefly, equal amounts of cell line and reference DNA were directly labeled with Cy3 and Cy5, respectively, using the SureTag Labeling Kit (Agilent Technologies) and hybridized in the presence of human Cot1-DNA (Life Technologies) to the array for 40 hours. The array was scanned using an Agilent array scanner and data was extracted using Feature Extraction (FE) software v10.10. For data analysis we used two different global analysis methods: Aberration Detection Module-2 (ADM-2, Agilent Technologies) and Circular Binary Segmentation (CBS).

Stires H., Heckler M.M., Fu X., Zhao L., Grasso C.S., Quist M.J., Lewis J.A., Klimach U., Zwart A., Mahajan A., Győrffy B., Cavalli L.R, & Riggins R.B. (2017). Integrated Molecular Analysis of Tamoxifen-Resistant Invasive Lobular Breast Cancer Cells Identifies MAPK and GRM/mGluR Signaling as Therapeutic Vulnerabilities. Molecular and cellular endocrinology, 471, 105-117.

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Comprehensive Genomic Profiling Using CGH

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DNA was isolated and labelled using Agilent-recommended protocol. CGH was performed on an Agilent Microarray platform with 105k probes (Agilent Inc., Santa Clara, CA). Array image was acquired with an Agilent Array Scanner. Microarray data was analyzed using the Cytogenomics software package from Agilent Inc. Interpretation of detected CNVs was conducted according to the ACMG standards and guidelines revision 2013 [13 (link)], and technical standards recommendation by ACMG and ClinGen [14 (link)]. Information for clinical significance on reported cases was extracted from Databases of Genomic Variants (ClinVar) at www.ncbi.nim.nih.gov/clinvar, and DECIPHER at www.decipher.sanger.ac.uk. Association analysis of gene function and clinical features is based on the information from Online Mendelian Inheritance in Man (OMIM at www.omim.org).

Chen T.J., Song R., Janssen A, & Yosypiv I.V. (2021). Cytogenomic Aberrations in Isolated Multicystic Dysplastic Kidney in Children. Pediatric research, 91(3), 659-664.

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Comprehensive Genomic Profiling Using CGH

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Chen T.J., Song R., Janssen A, & Yosypiv I.V. (2021). Cytogenomic Aberrations in Isolated Multicystic Dysplastic Kidney in Children. Pediatric research, 91(3), 659-664.

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MicroRNA Microarray Analysis Pipeline

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Total RNA was extracted using TRIzol (Invitrogen Life Technologies) according to the manufacturer’s instruction. RNA quality was assessed by using the Agilent 2100 bioanalyzer (Agilent Technologies), and only samples with RNA integrity number >8 were used. MicroRNA microarray Assay was done using miRbase version 21.0 by LC Sciences (LC Sciences, Houston, TX). Array experiments were conducted according to the manufacturer’s instructions. Briefly, the miRNAs were labeled with Agilent miRNA labeling reagent (Agilent Technologies). Then, dephosphorylated RNA was linked with pCp-y3 and the labeled RNA was purified and hybridized to the miRNA microarray. Images were scanned with the Agilent array scanner (Agilent Technologies) using a grid file and analyzed with Agilent feature extraction software version 10.10.
GeneSpring software V12 (Agilent Technologies) was used for summarization, normalization, and quality control of miRNA microarray data. The miRNA array data were calculated by first subtracting the background value and then normalizing the signals by locally weighted regression. The express levels of miRNAs were designated as statistically significant when the 2-tailed P value was ≤0.05. And signals <500 were interpreted as false-positive result. The statistically significant messenger RNAs were selected based on the fold change and adjusted P value ≤0.05.

Hu Z.Q., Rao C.L., Tang M.L., zhang Y., Lu X.X., Chen J.G., Mao C., Deng L., Li Q, & Mao X.H. (2019). Rab32 GTPase, as a direct target of miR-30b/c, controls the intracellular survival of Burkholderia pseudomallei by regulating phagosome maturation. PLoS Pathogens, 15(6), e1007879.

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