Genearray scanner

Manufactured by Agilent Technologies

Sourced in United States

The GeneArray scanner is a lab equipment product from Agilent Technologies. It is designed to analyze gene expression data from DNA microarray experiments. The core function of the GeneArray scanner is to capture high-resolution images of microarray slides and convert the data into a digital format for further analysis.

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GeneArray Scanner 3000 7G (3 citations) GeneArray Scanner G2500A (3 citations)

11 protocols using genearray scanner

Transcriptomic Analysis of Dopamine Pathways

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The expression profile of dopamine-related genes was assessed using HG-U133A 2.0 microarrays (Affymetrix, Santa Clara, CA, USA), the GeneChip™ 3′IVT PLUS, and Ge-neChip™ HT 3′IVT PLUS Reagent kits (ThermoFisher Scientific, Waltham, MA USA, Cat No. 902416, 902417). Fluorescence intensity was measured with the Gene Array scanner (Agilent Technologies, Santa Clara, CA, USA). The phrase “dopamine” was entered in the Affymetrix NetAffx™ Analysis Center database (http://www.affymetrix.com/analysis/index.affx; accessed on 1 August 2021) to obtain probe names and identification numbers.
The expression profile of miRNAs in endometrial tissue samples was determined using GeneChip miRNA 2.0 microarrays (Affymetrix, Santa Clara, CA, USA), according to the manufacturer’s protocol. The GeneChip Scanner 3000 7G (Agilent Technologies, Santa Clara, CA, USA) was used to scan the microarrays. A TargetScan prediction tool (http://www.targetscan.org, accessed on 1 August 2021) was then used to determine which miRNAs differentiating endometrial cancer from the control could potentially affect the expression of dopamine-related mRNAs.

Czerwiński M., Bednarska-Czerwińska A., Zmarzły N., Boroń D., Oplawski M, & Grabarek B.O. (2021). miRNAs in the Expression Regulation of Dopamine-Related Genes and Proteins in Endometrial Cancer. Journal of Clinical Medicine, 10(21), 4939.

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Endothelin Expression Profiling via Microarray

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Expression profile of endothelins and their receptors was determined using the GeneChip 3′IVT PLUS Reagent Kit (ThermoFisher Scientific, Waltham, MA, USA) and HG-U133A 2_0 oligonucleotide microarrays (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. Fluorescence signals were acquired by the GeneArray scanner (Agilent Technologies, Santa Clara, CA, USA). The methodology has been described in detail in other articles (Grabarek et al. 2021 (link)). Microarray experiment was further validated with RT-qPCR.

Zmarzły N., Januszyk S., Mieszczański P., Morawiec E., Buda P., Dziobek K., Opławski M, & Boroń D. (2022). Endothelin-3 is epigenetically silenced in endometrioid endometrial cancer. Journal of Cancer Research and Clinical Oncology, 149(9), 5687-5696.

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miRNA Transcriptome Analysis via Microarray

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Changes in the miRNA transcriptome in the test samples in comparison with the control samples were determined using the miRNA microarray technique GeneChip miRNA 2.0 Array (Affymetrix), as described by the manufacturer. Data were analyzed using a microarray scanning GeneArray scanner (Agilent Technologies).
Predictive evaluation of the effect of selected miRNAs on mRNAs were significantly differentiated in test samples from control samples was performed using the TargetScan database (http://www.targetscan.org; accessed on February 15, 2022) (29 (link)) and miRanda (http://mirdb.org; accessed on15 February 2022) (30 (link), 31 (link)). According to the miRDB database, “This is an online database for miRNA target prediction and functional annotations. All the targets in miRDB were predicted using a bioinformatics tool, MirTarget, which was developed by analyzing thousands of miRNA-target interactions from high-throughput sequencing experiments. Common features associated with miRNA binding and target downregulation have been identified and are used to predict miRNA targets with machine learning methods. A predicted target with a prediction score of >80 is most likely to be real; however, if the score is below 60, then one needs to exercise caution, and it is recommended to have other supporting evidence as well” (30 (link), 31 (link)).

Opławski M., Średnicka A., Niewiadomska E., Boroń D., Januszyk P, & Grabarek B.O. (2022). Clinical and molecular evaluation of patients with ovarian cancer in the context of drug resistance to chemotherapy. Frontiers in Oncology, 12, 954008.

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Microarray Analysis of Drug Resistance

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The microarray profile of mRNA expression changes that are associated with drug resistance was determined using the HG-U133A 2_0 microarray (Affymetrix, Santa Clara, CA, USA), the GeneChip™ 3′ IVT PLUS Reagent Kit, and GeneChip™ HT 3′ IVT PLUS Reagent Kit (Thermo Fisher Scientific, Waltham, MA USA, Cat. no. 902416) according to the manufacturer’s recommendations. The mRNA names and their ID number were determined from the Affymetrix NetAffx™ Analysis Center database after entering the phrase “drug resistance” (http://www.affymetrix.com/analysis/index.affx; accessed on February 2, 2022). Data were analyzed using a microarray scanning GeneArray scanner (Agilent Technologies, Santa Clara, CA, USA).

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Transcriptomic Profiling of Murine Adipose Tissue

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Total RNA was extracted from murine WAT (Subcutaneous region) and BAT (intrascapular) using ribopure RNA extraction kit (Invitrogen, USA) according to manufacturer's instructions. The quantification (total amount) and qualitative ratio metric analysis of RNA was done using Infinite M200 ProNanoQuant(Tecan, Switzerland). Integrity of the RNA samples were evaluated using 1.4% agarose gel. All RNA samples were found to be pure with no signs of degradation caused due to the extraction process. The entire microarray experiment was performed as per the protocol and guidelines provided by Affymetrix, Inc. (Santa Clara, CA). The microarray versions that were used in these studies were mouse 430.2.0 Affymetrix array. Briefly, first-strand of cDNA was generated from 500ng of RNA using a T7-linked oligo (dT) primer followed by second strand synthesis. Then, In vitro transcription was performed to synthesize aRNA incorporated with biotin-conjugated nucleotides and 15 μg of aRNA was fragmented prior to hybridization. The hybridized arrays were washed and stained with streptavidin-phycoerythrin using Affymetrix Fluidics Station 400 and finally scanned on Agilent GeneArray scanner. The microarray data is available on NCBI’s GEO database (Geo accession: GSE67389).

Baboota R.K., Sarma S.M., Boparai R.K., Kondepudi K.K., Mantri S, & Bishnoi M. (2015). Microarray Based Gene Expression Analysis of Murine Brown and Subcutaneous Adipose Tissue: Significance with Human. PLoS ONE, 10(5), e0127701.

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EMT Gene Expression Profiling

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The evaluation of the expression pattern of mRNAs connected with the EMT was done using oligonucleotide microarray microarrays HG-U133A 2_0 (Affymetrix, Santa Clara, CA, USA), the GeneChip™ 3′IVT PLUS Reagent Kit, and GeneChip™ HT 3′IVT PLUS Reagent Kit (ThermoFisher, Catalog Number 902416) according to the manufactures’ protocol. The names of the probes and their ID number were obtained from the Affymetrix NetAffx™ Analysis Center database after entering the phrase “EMT” (http://www.affymetrix.com/analysis/index.affx; accessed on 25 November 2020). Data were analyzed via using microarray scanning GeneArray scanner (Agilent Technologies, Santa Clara, CA, USA).

Opławski M., Nowakowski R., Średnicka A., Ochnik D., Grabarek B.O, & Boroń D. (2021). Molecular Landscape of the Epithelial–Mesenchymal Transition in Endometrioid Endometrial Cancer. Journal of Clinical Medicine, 10(7), 1520.

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Biogenic Amine Gene Expression Profiling

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The biogenic amine-related gene expression profile was determined using HG-U133A 2.0 oligonucleotide microarrays (Affymetrix, Santa Clara, CA, USA), the GeneChip™ 3′IVT PLUS Reagent Kit (ThermoFisher, Waltham, MA, USA, Cat. No. 902416), and the GeneChip™ HT 3′IVT PLUS Reagent Kit (ThermoFisher, Waltham, MA, USA, Cat. No. 902417).
The names of the probes and their identification numbers were obtained by entering the phrase “biogenic amine” in the Affymetrix NetAffx™ Analysis Center database (http://www.affymetrix.com/analysis/index.affx; accessed on 1 July 2021). Gene Array Scanner (Agilent Technologies, Santa Clara, CA, USA) was used to measure the fluorescence intensity.

Czerwiński M., Bednarska-Czerwińska A., Zmarzły N., Boroń D., Oplawski M, & Grabarek B.O. (2021). Evaluation of the Differences in the Expression of Biogenic Amine-Related mRNAs and Proteins in Endometrioid Endometrial Cancer. Journal of Clinical Medicine, 10(21), 4872.

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Transcriptome Analysis of Leptin Genes

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The expression profile of leptin-related genes was determined with HG-U133A 2_0 oligonucleotide microarrays (Affymetrix, Santa Clara, CA, USA), the GeneChip™ 3′IVT PLUS Reagent Kit, and the GeneChip™ HT 3′IVT PLUS Reagent Kit (ThermoFisher, Cat No. 902416). The Affymetrix NetAffx™ Analysis Center database (http://www.affymetrix.com/analysis/index.affx; accessed on 1 October 2020) was used to acquire the probe names and their identification numbers after entering the phrase “leptin”. A GeneArray scanner (Agilent Technologies, Santa Clara, CA, USA) for microarray scanning was used to analyze the obtained data.

Boroń D., Nowakowski R., Grabarek B.O., Zmarzły N, & Opławski M. (2021). Expression Pattern of Leptin and Its Receptors in Endometrioid Endometrial Cancer. Journal of Clinical Medicine, 10(13), 2787.

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Affymetrix Gene Expression Profiling

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Biotin-labeled cRNA was prepared by in vitro transcription using BioArray High Yield RNA Transcript Labeling Kit (ENZO Life Sciences, Inc., Farmingdale, NY) following the standard Affymetrix protocols. Biotinylated cRNAs were cleanup, quantified and 15 μg were fragmented and added to a hybridization cocktail according to Affymetrix procedures.
After quality determination on Test-3 arrays, the samples were hybridized using the GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 h at 45 °C to GeneChip Human Genome U133 set (HG-U133A and HG-U133B). The arrays were washed and stained with streptavidin–phycoerythrin using the Affymetrix antibody amplification protocol for eukaryotic targets (EukGE-WS2 protocol) in the GeneChip Fluidics Station 400 (Affymetrix, Santa Clara, CA). Images were acquired using the GeneArray Scanner (Agilent Technologies, Palo, CA), and row data were collected and analyzed by using the Affymetrix Micro Array Suite (MAS) version 5.0 software.

Agretti P., De Marco G., Ferrarini E., Di Cosmo C., Montanelli L., Bagattini B., Chiovato L, & Tonacchera M. (2021). Gene expression profile in functioning and non-functioning nodules of autonomous multinodular goiter from an area of iodine deficiency: unexpected common characteristics between the two entities. Journal of Endocrinological Investigation, 45(2), 399-411.

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Profiling TNF-α Signaling Genes via Microarray

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HG-U133A 2_0 oligonucleotide microarrays (Affymetrix, Santa Clara, CA, USA) and the GeneChip™ HT 3′IVT PLUS Reagent Kit (ThermoFisher, Waltham, MA, USA, Cat No. 902417) were used to determine the expression profile of genes involved in TNF-α signaling. 8 µg of RNA was used as a template to synthesize cDNA with SuperScript Choice System (Invitrogen Technologies, Carlsbad, CA, USA). BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY, USA) was then used to synthesize biotinylated cRNA. It was later purified with RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). The next step included fragmentation of the biotin-labeled cRNA with the Sample Cleanup Module Kit (Qiagen GmbH, Hilden, Germany). After hybridization to the microarray, cRNA was stained with streptavidin–phycoerythrin. A GeneArray scanner (Agilent Technologies, Santa Clara, CA, USA) was used to acquire the fluorescence signals. The list of genes related to TNF-α signaling was prepared based on data from the PathCards database (http://pathcards.genecards.org/) accessed on April 27, 2022 (Belinky et al. 2015 (link)).

Zmarzły N., Januszyk S., Mieszczański P., Czarniecka J., Bednarska-Czerwińska A., Boroń D., Oplawski M, & Grabarek B.O. (2023). The influence of selected microRNAs on the expression profile of genes and proteins related to the tumor necrosis factor-alpha signaling pathways in endometrioid endometrial cancer. Journal of Cancer Research and Clinical Oncology, 149(12), 9679-9689.

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