Genearray scanner g2500a

Manufactured by Hewlett-Packard

Sourced in United States

The GeneArray Scanner G2500A is a high-performance microarray scanner designed for gene expression analysis. It features a compact design and advanced optics to capture precise and reliable data from gene expression microarrays.

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Lab products found in correlation

Fluidics station 400, by Hewlett-Packard (1 mentions) Rneasy midi kit, by Qiagen (1 mentions) Command console, by Thermo Fisher Scientific (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Rneasy kit, by Qiagen (1 mentions) Superscript choice system, by Thermo Fisher Scientific (1 mentions) Fluidics station 400, by Thermo Fisher Scientific (1 mentions) Affymetrix expression analysis technical manual, by Thermo Fisher Scientific (1 mentions)

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GeneArray Scanner

4 protocols using genearray scanner g2500a

Genome-wide Gene Expression Profiling

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Total RNA was extracted from 7 days vehicle or of TGF-β1 treated cells using RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix, Santa Clara, CA USA). Following fragmentation, cRNA was hybridized on GeneChip Rat Genome 230 2.0 Array (experiment 1) as well as on GeneChip Rat Expression 230A Array (experiment 2). For both experiments, GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and then scanned using the Hewlett-Packard GeneArray Scanner G2500A. The expression profiling and data analysis of the two independent experiments were carried out at the competence centre for fluorescent bioanalytics (KFB; Regensburg, Germany).

Kandasamy M., Lehner B., Kraus S., Sander P.R., Marschallinger J., Rivera F.J., Trümbach D., Ueberham U., Reitsamer H.A., Strauss O., Bogdahn U., Couillard-Despres S, & Aigner L. (2014). TGF-beta signalling in the adult neurogenic niche promotes stem cell quiescence as well as generation of new neurons. Journal of Cellular and Molecular Medicine, 18(7), 1444-1459.

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Transcriptomic Analysis of hESCs

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Total mRNA was isolated from hESCs using the RNeasy kit (Qiagen). The quality of the total RNA was confirmed using an Agilent 2100 Bioanalyzer. Samples were sent to the Pan Facility at Stanford University for further processing. Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 6 μg of total RNA (GeneChip Whole-Transcript Sense Target-Labeling Assay, 701880 Rev.5, Affymetrix). The samples were then hybridized to the Human Gene 2.0 ST array. Probe arrays were washed and scanned with the Hewlett-Packard GeneArray Scanner G2500A. Raw data files were created by Command Console, the Affymetrix operating software program. The Affymetrix Expression Console Program was used to examine the Affymetrix Gene Array quality control factors for all samples in a project. Global scaling was used as the normalization method (RMA). Enrichment analysis was performed with cWords.

Durruthy-Durruthy J., Sebastiano V., Wossidlo M., Cepeda D., Cui J., Grow E.J., Davila J., Mall M., Wong W.H., Wysocka J., Au K.F, & Pera R.A. (2015). The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming. Nature genetics, 48(1), 44-52.

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Biotin-Labeled cRNA Hybridization to Affymetrix GeneChip

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The SuperScript Choice system (Invitrogen, Carlsbad, CA, USA) was used for transcription of total RNA into double-stranded cDNA. To assembly first-strand cDNA synthesis a T7-(dT24) oligonucleotide primer with a RNA polymerase promoter site was used. In vitro transcription followed after second-strand synthesis in the presence of biotin-11-cytidine triphosphate and biotin-16-uridine triphosphate (Enzo Diagnostics, New York, NY, USA). Next, biotin-labelled cRNA were fragmented (20 μg at 94°C for 35 minutes) and added to a hybridization solution to a final cRNA concentration (0.05 mg/mL). The solution was incubated for hybridization with an oligonucleotide array (AffymetrixGeneChip [Hu133A]), containing 22,283 probe sets for known genes or expressed sequence tags (ESTs). After staining with streptavidin-phycoerythrin a Gene Array scanner G2500A (Hewlett Packard, Palo Alto, CA, USA) was used for scanning of the hybridisation products according to the recommendations of the manufacturer.

Hass H.G., Vogel U., Scheurlen M, & Jobst J. (2017). Subclassification and Detection of New Markers for the Discrimination of Primary Liver Tumors by Gene Expression Analysis Using Oligonucleotide Arrays. Gut and Liver, 12(3), 306-315.

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miRNA Microarray Profiling Protocol

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Microarray services were provided by the Penn Microarray Facility. All protocols were conducted as described in the standard Affymetrix Expression Analysis Technical Manual (Affymetrix Inc., Santa Clara, CA). Briefly, biotinylated cRNA was prepared from 100 ng total RNA; following fragmentation, cRNA was hybridized for 16 h at 45°C on the Affymetrix miRNA-specific arrays. Microarrays were then washed at low (6X SSPE) and high (100 mM MES, 0.1 M NaCl) stringency and stained with streptavidin-phycoerythrin in an Affymetrix Fluidics Station 400. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner (Hewlett-Packard Gene Array Scanner G2500A) was used to collect fluorescence signal after excitation at 570 nm.

Genini S., Guziewicz K.E., Beltran W.A, & Aguirre G.D. (2014). Altered miRNA expression in canine retinas during normal development and in models of retinal degeneration. BMC Genomics, 15(1), 172.

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