Agilent scanner

Manufactured by Agilent Technologies

Sourced in United States

The Agilent scanner is a high-performance laboratory equipment designed for scanning and digitizing various samples. It captures detailed images with precision and clarity, enabling comprehensive analysis and data collection.

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Agilent High-Resolution Microarray Scanner (5 citations) Agilent DirectDrive scanner (5 citations) Agilent’s DNA microarray scanner (6 citations) Agilent Scanner G2505C microarray scanner (2 citations) Agilent G2565AA microarray scanner (2 citations) Agilent SureScan Microarray Scanner (20 citations) Agilent Scanner G2565CA (15 citations) Agilent Microarray Scanner (G2565CA) (30 citations) Agilent Scanner version C (2 citations) Agilent Single-Color DNA Microarray Scanner (2 citations)

115 protocols using agilent scanner

Microarray Analysis of HCC Tissues

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For performing the microarray analysis, 3 paired of tumor tissues and nontumor tissues were obtained from HCC patients. Then total RNAs were collected from them and were transferred into the fluorescent cRNA by using an Arraystar Super RNA Labeling Kit (Arraystar, USA). Moreover, they were purified by RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Additionally, the microarray hybridizations on Arraystar Human circRNA Array chip (Agilent, USA) were performed according to its protocol. Finally, it was scanned by an Agilent Scanner (Agilent, Santa Clara, CA, USA), which was analyzed with the Agilent supporting software.

Chen J, & Qi Z. (2022). The Elevated Circ_0067835 Could Accelerate Cell Proliferation and Metastasis via miR-1236-3p/Twist2 Axis in Hepatocellular Carcinoma. BioMed Research International, 2022, 2825172.

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Microarray Analysis of Stemness Genes

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Total RNA was prepared using TriPure Isolation Reagent (Roche Life Science). cRNA was amplified and labelled using a Quick Amp Labelling Kit (Agilent Technologies) and hybridized to a 8 × 60 k v2 array chips (Agilent Technologies) according to the manufacturer’s instructions. The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies). The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies. Briefly, a signal intensity less than 1 was corrected to 1 (not detected), and then the 75th percent shift normalization was conducted. Unless otherwise specified, data processing and analysis were performed using the statistical software R. Gene Set Enrichment Analysis (GSEA)60 (link) was performed according to the standard procedure. Stemness gene set was adopted from the publication by Munoz, J et al.46 (link).

Chang P.H., Sekine K., Chao H.M., Hsu S.H, & Chern E. (2017). Chitosan promotes cancer progression and stem cell properties in association with Wnt signaling in colon and hepatocellular carcinoma cells. Scientific Reports, 7, 45751.

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Gene Expression Profiling of Multiple Sclerosis

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The gene expression profiling was performed by following standard protocols in CPS [24 (link)]. Briefly, the BMSCs from 3 age-matched SM patients (30.3±8.5 years) and healthy donors (34.7±6.8 years) were selected for analysis. Total RNA was extracted and labeled with Cy5-CTP and human reference RNA (was labeled with Cy3-CTP. The labeled cRNA was pooled, fragmented and then hybridized on 4 × 44K microarrays (Agilent, Santa Clara, CA) for 17 hours at 65°C. The microarrays were then washed and scanned using an Agilent Scanner and data were acquired using Agilent Feature Extraction Software. The raw data was uploaded into mAdb database (http://madb.nci.nih.gov/) and then analyzed by BRB-Array Tools [26 (link)] (http://linus.nci.nih.gov/BRB-ArrayTools.html) and Partek Genomics Suite (Partek Inc, Saint Louis, MO). Tests for differences between MS patients and healthy donors were conducted for individual genes using a t-test, considering P values of <0.001 as significant. The functional relevance of the differentially expressed genes was annotated by using MetaCore database (https://portal.genego.com/) following its instructions.

Nemeth K., Wilson T.M., Ren J.J., Sabatino M., Stroncek D.F., Krepuska M., Bai Y., Robey P.G., Metcalfe D.D, & Mezey E. (2015). Impaired Function of Bone Marrow Stromal Cells in Systemic Mastocytosis. Stem cell research, 15(1), 42-53.

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Myogenic Differentiation Transcriptome Analysis

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Total RNA was prepared from DsRed+ cells, DsRed+ cells allowed to undergo myogenic differentiation for 5 days, DECT+ cells, and DECT+ cells allowed to undergo myogenic differentiation for 5 days. RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and purified as previously described (Ozawa and Kobayashi, 2014 (link)). cRNA was amplified and labeled using a Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and hybridized to a 44K Agilent 60-mer oligomicroarray (Mouse Oligo Microarray Kit). The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction Software (version 9.5.1.1). Microarray data analysis was supported by Cell Innovator (Fukuoka, Japan).

, & Ozawa M. (2015). E-cadherin cytoplasmic domain inhibits cell surface localization of endogenous cadherins and fusion of C2C12 myoblasts. Biology Open, 4(11), 1427-1435.

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MiRNA Profiling of FFPE Samples

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MiRNA profiling based on direct hybridization without sample amplification was performed on the set of 21 responders and 20 non-responders FFPE tissue samples using Agilent MiRNA MicroArrays (#G4470B; Agilent Technologies, Santa Clara, CA, USA). These microarrays consist of 60-mer DNA probes synthesized in situ and contain 15.000 features which represent 723 human miRNAs, sourced from the Sanger miRBASE database (Release 10.1). RNA labeling and hybridization were performed in accordance to manufacturer's indications. Agilent scanner and the Feature Extraction 10.5 software (Agilent Technologies) were used to obtain the microarray raw-data. Data transformation was applied to set all the negative raw values at 1.0, followed by a Quantile normalization and log2 transformation. Filters on gene expression were used to keep only the miRNAs expressed in at least one sample.

Mlcochova J., Faltejskova-Vychytilova P., Ferracin M., Zagatti B., Radova L., Svoboda M., Nemecek R., John S., Kiss I., Vyzula R., Negrini M, & Slaby O. (2015). MicroRNA expression profiling identifies miR-31-5p/3p as associated with time to progression in wild-type RAS metastatic colorectal cancer treated with cetuximab. Oncotarget, 6(36), 38695-38704.

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Comparative Genomic Hybridization Analysis

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CGH analysis was performed using our custom Agilent microarray (4×44K format)^{12 (link)}. Genomic DNA from wild type or mutants was digested with AluI and RsaI. After complete digestion, mutant DNA was labeled with Cy-5 dCTP (Amersham Biosciences) and wild type DNA was labeled with Cy-3 dCTP (Amersham Biosciences) using the BioPrime® Array CGH Genomic Labeling kit (Invitrogen). Equal amounts of labeled DNA (1.5 ug) were competitively hybridized onto the microarray. Prehybridization, probe hybridization, washing, and drying steps for arrays were performed as for ChIP-chip experiments^{12 (link)}. Arrays were scanned using an Agilent scanner (Agilent) and analyzed using Agilent Feature Extraction (Agilent). Signal intensity ratios between Cy5 (mutant) and Cy3 (Wild type) were calculated from rProcessedSignal and gProcessedSignal values according to Agilent Feature Extraction. The log2 transformed Cy5/Cy3 ratio is plotted along the chromosome.

Mizuguchi T., Fudenberg G., Mehta S., Belton J.M., Taneja N., Folco H.D., FitzGerald P., Dekker J., Mirny L., Barrowman J, & Grewal S.I. (2014). Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature, 516(7531), 432-435.

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Microarray Analysis of miRNA Expression

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One hundred nanograms of total RNA per sample was employed for microarray analysis (Human micro‐RNA Microarray V3, #G4470C, Agilent Technologies, Santa Clara, CA, U.S.A.). The chip allowed simultaneous analysis of 1,200 human miRNAs obtained from the Sanger miR‐BASE database (Release 10.1). RNA labeling and hybridization were performed according to the manufacturer's indications. Row data were obtained using an Agilent scanner and the Feature Extraction 10.5 software (Agilent Technologies).
The GeneSpring GX 12 software (Agilent Technologies) was employed to analyze microarray results. All negative values were transformed at 1.0, followed by Quantile normalization and log2 transformation. Differentially expressed miRNAs were identified by comparing autoptic controls with autoptic and bioptic epileptic samples, applying a twofold‐change filter, the Mann‐Whitney test, and Benjamini‐Hochberg correction (adjusted p < 0.05). Manhattan correlation was used for cluster analysis.

Roncon P., Zucchini S., Ferracin M., Marucci G., Giulioni M., Michelucci R., Rubboli G, & Simonato M. (2016). Is autopsy tissue a valid control for epilepsy surgery tissue in microRNA studies?. Epilepsia Open, 2(1), 90-95.

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Gene Expression Microarray Analysis

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The qualified RNA samples were labeled and hybridized on Agilent 4 × 44 K Custom design Gene Expression Microarray according to manufacturer protocol (Agilent, Santa Clara, CA). In brief, 100 ng of each RNA sample was amplified to cRNA and labeled with Cy-3 using Agilent Low Input Quick Amp Labeling Kit. The labeled samples were hybridized for 16 hours at 10 rotations per minute. After hybridization, the arrays were washed and scanned by Agilent scanner and then the image was analyzed by Agilent Feature Extraction v11.5. Data obtained from Feature Extraction were imported to GeneSpring GX version 13.1 (Agilent Technologies, Santa Clara, CA) for 75th percentile shift and baseline to median of all samples normalization.

Xu J., Wang J.X., Zhou J.M., Xu C.L., Huang B., Xing Y., Wang B., Luo R., Wang Y.C., You X.F., Lu Y, & Yu L.Y. (2017). A novel protein kinase inhibitor IMB-YH-8 with anti-tuberculosis activity. Scientific Reports, 7, 5093.

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Transcriptome Profiling of TGF-β1-Treated HaCaT Cells

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Total RNA of the non-treated HaCaT, TGF-β1-treated (20 ng/ml TGF-β1; treated for 48 h at 37˚C), TY1 tag-overexpressing and TY1-tagged SNAI2-overexpressing cells was extracted using a NucleoSpin RNA kit (Machrey-Nagel, GmBH & Co.). The cRNA was amplified and labeled using a Low-Input QuickAmp Labeling kit (Agilent Technologies, Inc.) and hybridized to a SurePrint G3 Human Gene Expression Microarray 8x60K v3 (Agilent Technologies, Inc.). The procedure was carried out as previously described (12-14 (link)). All hybridized microarray slides were scanned by an Agilent scanner, after which relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction Software (9.5.1.1). The raw signal intensities and flags for each probe were calculated and normalized by a quantile algorithm. Identification of differentially expressed genes was carried out by calculating Z-scores and non-log scaled fold-change ratios. Criteria for upregulated genes were Z-score >2.0 and ratio >2.0, whereas those for downregulated genes were Z-score <−2.0 and ratio <0.5. The DNA microarray datasets were deposited in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) at the National Center for Biotechnology Information (NCBI) with the accession numbers GSE166199 and GSE166200.

Miyake Y., Nagaoka Y., Okamura K., Takeishi Y., Tamaoki S, & Hatta M. (2021). SNAI2 is induced by transforming growth factor-β1, but is not essential for epithelial-mesenchymal transition in human keratinocyte HaCaT cells. Experimental and Therapeutic Medicine, 22(4), 1124.

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Canine Array-CGH Microarray Protocol

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Array-CGH was performed using a custom Agilent Canine Genome CGH Microarray 180 K (Agilent Technologies, Santa Clara, California, USA) and processed as reported [28] (link). Briefly, 500 ng of purified DNA of a subject and a control, were double-digested with RsaI and AluI for two hours at 37°C. After 20 minutes at 65°C, each digested sample was labeled by the Agilent random primers; labeling was performed for two hours using Cy5-dUTP for the subject DNA and Cy3-dUTP for the control DNA. The labeled products were columns purified and prepared according to the Agilent protocol. After probe denaturation and pre-annealing with 5 µl of Cot-1 DNA, hybridization was performed at 65°C, with rotation for 40 hours. After two washing steps, the arrays were analyzed with the Agilent scanner and the Feature Extraction software (v10.7.3.1). A graphical overview was obtained using the CGH analytics software (v7.0.4.0). The DNA extracted from a normal female (boxer breed) was used as the control in all cases. All experimental data were submitted to GEO repository with the following Series accession number: GSE57137.

Rossi E., Radi O., De Lorenzi L., Vetro A., Groppetti D., Bigliardi E., Luvoni G.C., Rota A., Camerino G., Zuffardi O, & Parma P. (2014). Sox9 Duplications Are a Relevant Cause of Sry-Negative XX Sex Reversal Dogs. PLoS ONE, 9(7), e101244.

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