G2505b micro array scanner

Manufactured by Agilent Technologies

Sourced in United States

The G2505B Micro Array Scanner is a lab equipment product from Agilent Technologies. It is designed to capture high-resolution images of microarray slides. The device features a compact and efficient design for reliable operation.

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12 protocols using g2505b micro array scanner

Profiling Mouse T-UCR Expression in Spinal Cord

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T-UCRs expression profiles in the spinal cord were assessed using Arraystar Mouse LncRNA Microarray V2.0 (8×60 K, Arraystar), which can profile the global expression of mice T-UCRs. For each sample, T7 Oligo (dT) primer containing T7 RNA polymerase promoter sequence was used to synthesize the first strand cDNA from total RNA by CbcScript reverse transcriptase. The RNase H-DNA polymerase I controlled the process of the second-strand cDNA synthesis (KangChen Bio-tech, China). T7 promoter drove the synthesis of cRNA using the above cDNA as the template. The cRNA were reverse-transcribed into cDNA again by random primers, and then the transcription products were labeled in the presence of Cy3-dCTP, random primers, and Klenow Enzyme. The microarray slides were hybridized at 45°C for 16 h in 2× GEx Hybridization Buffer HI-RPM (Agilent Technologies) containing the labeled cDNA. After being washed, microarray results were scanned by Agilent G2505B Microarray Scanner, and images were quantified using Agilent's Feature Extraction software (Agilent Technologies). Quantile normalization of raw data and subsequent data processing was performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

Jiang B.C., Yang T., He L.N., Tao Y.X, & Gao Y.J. (2016). Altered T-UCRs expression profile in the spinal cord of mice with neuropathic pain. Translational perioperative and pain medicine, 1(3), 1-10.

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Comparative Transcriptomics of Meso-CAFs and CAF-3

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Total RNA of Meso-CAFs and CAF-3 was extracted from primary cell cultures of about 80% confluence with RNeasy Mini Kit (Qiagen Sciences, Germantown, MD, USA) according to the respective protocol of the manufacturer. Whole-genome gene expression analysis was carried out as described previously by Pirker et al. [11 (link)] and Mathieu et al. [13 (link)] using 4x44K whole genome oligonucleotide-based gene expression microarrays (Agilent, Santa Clara, CA, USA) and a G2505B Micro Array Scanner (Agilent, Santa Clara, CA, USA). Gene expression data of Meso-CAFs was compared to CAF-3 and to data of 31 PM cell lines available from a previous publication [11 (link)]. Analysis and comparison of expression data was conducted in R [15 ], and differentially expressed genes between cell types (Meso-CAF, CAF-3, PM) were determined using “limma” package [16 (link)] as previously described by Mohr et al. [17 (link)]. Genes with multiple oligonucleotide probes on the array were summarized to the probe with maximal interquartile range using the package “genefilter” [18 ]. Additional plots were created using GraphPad Prism 8.0 (GraphPad Software, San Diego, CA, USA). Whole genome gene expression array data from Meso-CAFs and CAF-3 are available at ArrayExpress (https://www.ebi.ac.uk/biostudies/arrayexpress) under the accession number E-MTAB-12177.

Ries A., Flehberger D., Slany A., Pirker C., Mader J.C., Mohr T., Schelch K., Sinn K., Mosleh B., Hoda M.A., Dome B., Dolznig H., Krupitza G., Müllauer L., Gerner C., Berger W, & Grusch M. (2023). Mesothelioma-associated fibroblasts enhance proliferation and migration of pleural mesothelioma cells via c-Met/PI3K and WNT signaling but do not protect against cisplatin. Journal of Experimental & Clinical Cancer Research : CR, 42, 27.

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Whole Genome Expression Profiling via Microarray

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Isolation of total RNA and whole genome gene expression arrays were performed as described in [55 (link), 56 (link)]. Single or dual color experiments were performed according to the instructions provided by Agilent using the Quick Amp Labeling Kit. Slides were scanned with a G2505B Micro Array Scanner (Agilent). Feature extraction and data analysis were carried out using the Feature Extraction and GeneSpring software, respectively.

Spitzwieser M., Pirker C., Koblmüller B., Pfeiler G., Hacker S., Berger W., Heffeter P, & Cichna-Markl M. (2016). Promoter methylation patterns of ABCB1, ABCC1 and ABCG2 in human cancer cell lines, multidrug-resistant cell models and tumor, tumor-adjacent and tumor-distant tissues from breast cancer patients. Oncotarget, 7(45), 73347-73369.

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Transcriptome Analysis of Floral Tissues

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Total RNA was isolated from individual floral tissues including petals, pistils, stamens, and the pith using an RNeasy Plant Mini Kit (QIAGEN). The RNA samples were quantified using an ND-1000 spectrophotometer (NanoDrop Technologies) and the quality was confirmed with an Experion System (Bio-Rad Laboratories). The cRNA was then amplified, labeled, and hybridized to a 4 × 44k Agilent 60-mer custom oligomicroarray according to the manufacturer’s instructions. The probes on this custom array were designed based on our in-house cDNA database, which was prepared from female-stage spadices of S. renifolius. All hybridized microarray slides were scanned using a G2505B Microarray Scanner (Agilent). Relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction Software (9.5.1.1), and the microarray data have been deposited in the NCBI Gene Expression Omnibus repository with the accession number GSE68011.

Ito-Inaba Y., Masuko-Suzuki H., Maekawa H., Watanabe M, & Inaba T. (2016). Characterization of two PEBP genes, SrFT and SrMFT, in thermogenic skunk cabbage (Symplocarpus renifolius). Scientific Reports, 6, 29440.

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Glycosylation Profiling of Immobilized Human Mucins

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To analyze the glycosylation profiles of the immobilized human mucins, the microarray slides were incubated with a panel of tetramethylrhodamine isothiocyanate (TRITC)-labeled lectins (Supplementary Table S4). All incubation procedures were carried out in the dark. Lectins were incubated at the indicated concentration in TBST (Supplementary Table S4) on the mucin using an eight well gasket and incubation cassette system (Agilent Technologies, Dublin, Ireland) for 1 h at 37 °C in the dark with gentle rotation (4 rpm). Following incubation, slides were washed three times in low salt Tris buffered saline (20 mM Tris, 100 mM NaCl, 1 mM CaCl₂, 1 mM MgCl₂, pH 7.2, TBS) supplemented with 0.05% Tween 20 (TBST), then once in TBS and once in deionized water and dried by centrifugation as above. Microarrays were scanned immediately in an Agilent G2505B microarray scanner (532 nm laser, 90% PMT and 5 μm resolution). Images were saved as *.tif files for data extraction.

Dunne C., Naughton J., Duggan G., Loughrey C., Kilcoyne M., Joshi L., Carrington S., Earley H., Backert S., Robbe Masselot C., May F.E, & Clyne M. (2018). Binding of Helicobacter pylori to Human Gastric Mucins Correlates with Binding of TFF1. Microorganisms, 6(2), 44.

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DNA Microarray Analysis of CTCL Cell Lines

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DNA was isolated from the CTCL cell lines using the QiaAmp DNA Blood Mini kit (Qiagen). Normal human reference DNA from multiple anonymous male donors was used as the reference DNA (Promega). Labeling and hybridization procedures were performed using the SureTag DNA Labelling kit, according to instructions (Agilent Technologies, USA). Equal quantities of fluorescently labeled DNA were mixed and co‐hybridized to a 44 K DNA microarray (G4426B‐014950, Agilent Technologies). After hybridization and washing, according to the manufacturer's protocol, scanning was performed on a G2505B Micro Array Scanner (Agilent Technologies). Feature extraction and data analysis were carried out using Feature Extraction (version 10.7.3.1) and Agilent Genomic Workbench version 7, respectively (Agilent Technologies). The ADM‐1 algorithm and a threshold of 6 were applied, and borders for aberrations were set to ±0.25 (log₂ ratio) with a minimum number of three probes per region (default settings recommended by Agilent Technologies).

Sorger H., Dey S., Vieyra‐Garcia P.A., Pölöske D., Teufelberger A.R., de Araujo E.D., Sedighi A., Graf R., Spiegl B., Lazzeri I., Braun T., Garces de los Fayos Alonso I., Schlederer M., Timelthaler G., Kodajova P., Pirker C., Surbek M., Machtinger M., Graier T., Perchthaler I., Pan Y., Fink‐Puches R., Cerroni L., Ober J., Otte M., Albrecht J.D., Tin G., Abdeldayem A., Manaswiyoungkul P., Olaoye O.O., Metzelder M.L., Orlova A., Berger W., Wobser M., Nicolay J.P., André F., Nguyen V.A., Neubauer H.A., Fleck R., Merkel O., Herling M., Heitzer E., Gunning P.T., Kenner L., Moriggl R, & Wolf P. (2022). Blocking STAT3/5 through direct or upstream kinase targeting in leukemic cutaneous T‐cell lymphoma. EMBO Molecular Medicine, 14(12), e15200.

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Genomic DNA Isolation and Array CGH Analysis

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Isolation of genomic DNA and array CGH analysis were performed as described in [55 (link)] using 4 × 44K whole genome oligonucleotide-based arrays (Agilent, Canada). Labeling and hybridization procedures were performed according to the instructions provided by Agilent using the SureTag DNA Labeling Kit. Slides were scanned with a G2505B Micro Array Scanner (Agilent). Feature Extraction and data analysis were carried out using the Feature Extraction and Agilent Genomic Workbench software, respectively.

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Array CGH Analysis of Meso-CAFs and CAF-3

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Microarray-based comparative genomic hybridization (array CGH) analysis of Meso-CAFs and CAF-3 was performed as described by Pirker et al. [11 (link)] and Mathieu et al. [13 (link)]. Genomic DNA was isolated from primary fibroblast cultures of about 80% cell confluence using QIAamp DNA Blood Mini Kit (Qiagen, Valencia, CA, USA). The genome analysis was carried out on 4x44K whole genome oligonucleotide-based microarrays (Agilent, Santa Clara, CA, USA) according to the manufacturer’s protocol, scanned on a G2505B Micro Array Scanner (Agilent, Santa Clara, CA, USA) and analyzed using the software Genomic Workbench (version 7.0) (Agilent, Santa Clara, CA, USA). Array CGH profiles of fibroblasts were checked for genomic alterations and compared to genome profiles of PM cell lines from a previous publication [11 (link)]. Array CGH data from Meso-CAFs and CAF-3 are available at ArrayExpress (https://www.ebi.ac.uk/biostudies/arrayexpress) under the accession number E-MTAB-12179.

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Mouse miRNA microarray analysis

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Total RNA was extracted by using the miRNeasy Mini Kit (Qiagen, Tokyo, Japan). The quality of the RNA samples was assessed using the Agilent 2100 Bioanalyzer 2100 (Agilent, Santa Clara, USA). The microRNA microarray analysis was performed with a Mouse miRNA microarray 8 × 15K Rel. 15.0 (Agilent, #29152). The fluorescence intensity was measured with a G2505B Micro Array Scanner (Agilent) in the Institute for Gene Research, Kanazawa University (Ishikawa, Japan). The data were normalized using the quantile method with GeneSpring 12.6.1 GX software (Agilent). The raw data are available in the Gene Expression Omnibus (GEO) (GSE77222).

Yoshida A., Kitajima S., Li F., Cheng C., Takegami Y., Kohno S., Wan Y.S., Hayashi N., Muranaka H., Nishimoto Y., Nagatani N., Nishiuchi T., Thai T.C., Suzuki S., Nakao S., Tanaka T., Hirose O., Barbie D.A, & Takahashi C. (2017). MicroRNA-140 mediates RB tumor suppressor function to control stem cell-like activity through interleukin-6. Oncotarget, 8(8), 13872-13885.

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Genome-wide mRNA Expression Analysis

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mRNA of RKOp53wt and RKOp53KO cells was isolated with an RNeasy Mini Kit from Qiagen (Hilden, Germany) according to the manufacturer’s instructions. Quality and integrity of mRNA was checked on the Agilent 2100 Bioanalyzer, and only samples with RIN values >9 were included for microarray analysis. Whole genome oligonucleotide-based gene expression microarray analysis was performed using the 4 × 44 K microarray format as described previously [48 (link)]. Dual-color experiments were performed using the Quick Amp Labelling Kit according to the instructions provided (Agilent, Santa Clara, CA, USA). Slides were scanned on a G2505B Micro Array Scanner (Agilent). Feature Extraction and data analysis were carried out using the Feature Extraction and GeneSpring software (both Agilent).

Dinhof C., Pirker C., Kroiss P., Kirchhofer D., Gabler L., Gojo J., Lötsch-Gojo D., Stojanovic M., Timelthaler G., Ferk F., Knasmüller S., Reisecker J., Spiegl-Kreinecker S., Birner P., Preusser M, & Berger W. (2020). p53 Loss Mediates Hypersensitivity to ETS Transcription Factor Inhibition Based on PARylation-Mediated Cell Death Induction. Cancers, 12(11), 3205.

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