Affymetrix genechip scanner 7g

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Affymetrix GeneChip Scanner 7G is a high-performance microarray scanner designed for the analysis of DNA and RNA samples. It is capable of scanning and detecting fluorescent signals from GeneChip arrays, providing users with accurate and reliable data for gene expression analysis and other genomic applications.

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Lab products found in correlation

Nanodrop one, by Thermo Fisher Scientific (4 mentions) Genechip fluidics station 450, by Thermo Fisher Scientific (3 mentions) Genechip wt pico reagent kit, by Thermo Fisher Scientific (2 mentions) Agilent 2100 bioanalyzer g2939a, by Agilent Technologies (2 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Lysis buffer, by Qiagen (1 mentions) Bead beater, by Biospec (1 mentions) Rnalater, by Thermo Fisher Scientific (1 mentions) Rneasy kit, by Qiagen (1 mentions) Mouse gene 2.0 st array, by Thermo Fisher Scientific (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions)

6 protocols using affymetrix genechip scanner 7g

Porcine Transcriptome Profiling via Microarray

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First, we assessed the RNA integrity using a bioanalyzer (2100 Bioanalyzer, Agilent, Santa Clara, CA, USA). We determined the RNA concentration using Nanodrop One (Thermofisher, Waltham, MA, USA). Biotin-labeled ss-cDNA was synthesized from total RNA with a GeneChip™ WT Pico Reagent Kit (Thermo Fisher Scientific, Waltham, MA, USA), fragmented, and subsequently hybridized using porcine arrays (Thermo Fisher Scientific, Waltham, MA, USA). Afterward, the chips were washed and scanned by the Affymetrix GeneChip Scanner 7G (Thermofisher, Waltham, MA, USA). One control group sample was later identified as an outlier and therefore excluded from the analysis.

Saemann L., Wächter K., Georgevici A.I., Pohl S., Hoorn F., Veres G., Korkmaz-Icöz S., Karck M., Simm A, & Szabó G. (2024). Transcriptomic Changes in the Myocardium and Coronary Artery of Donation after Circulatory Death Hearts following Ex Vivo Machine Perfusion. International Journal of Molecular Sciences, 25(2), 1261.

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Porcine LAD Transcriptome Analysis

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We determined the LAD transcriptome using porcine arrays (Thermo Fisher Scientific, Waltham, MA, USA). First, we assessed the RNA integrity using the Bioanalyzer (2100 Bioanalyzer, Agilent, Santa Clara, CA, USA). Then, the RNA concentration was determined using a Nanodrop One (Thermofisher, Waltham, MA, USA). Biotin-labeled ss-cDNA was synthesized from total RNA with a GeneChip™ WT Pico Reagent Kit (Thermo Fisher Scientific, Waltham, MA, USA), fragmented, and subsequently hybridized using porcine arrays (Thermo Fisher Scientific, Waltham, MA, USA). Then, we washed the chips. The chips were scanned by the Affymetrix GeneChip Scanner 7G (Thermofisher, Waltham, MA, USA). One control group sample was identified as an outlier based on PCA and was, therefore, excluded. Due to the high reliability of the microarray results based on the high number of N = 8 samples per group that were individually analyzed, we did not confirm selective gene expressions by qPCR.

Saemann L., Wächter K., Gharpure N., Pohl S., Hoorn F., Korkmaz-Icöz S., Karck M., Veres G., Simm A, & Szabó G. (2024). HTK vs. HTK-N for Coronary Endothelial Protection during Hypothermic, Oxygenated Perfusion of Hearts Donated after Circulatory Death. International Journal of Molecular Sciences, 25(4), 2262.

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RNA Extraction and Microarray Analysis in Mouse Lung

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At the time of analysis, the right upper lobe from three to four mice per group was excised from OCT, placed in RNAlater (Fisher Scientific) for 5 min, and homogenized in 2 ml lysis buffer (QIAGEN, Valencia, CA) with zirconia-silica beads using a BeadBeater (BioSpec Products, Bartlesville, OK). RNA isolation was performed using the QIAGEN RNeasy kit according to the manufacturer's protocol with slight modifications (Barry et al., 2010 (link)). For gene expression analysis, samples were not pooled. Total RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific–Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp Premier RNA Amplification Kit (Applied Biosystems–Ambion, Austin, TX) from total RNA, hybridized to GeneChip Mouse Genome 430 2.0 arrays in Affymetrix GeneChip hybridization oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara, CA).

Jackson I.L., Baye F., Goswami C.P., Katz B.P., Zodda A., Pavlovic R., Gurung G., Winans D, & Vujaskovic Z. (2017). Gene expression profiles among murine strains segregate with distinct differences in the progression of radiation-induced lung disease. Disease Models & Mechanisms, 10(4), 425-437.

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Comparative Transcriptome Analysis of APE1 Variants

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The Mouse Gene 2.0 ST array (Affymetrix) was used to profile global gene expression of three isogenic cell lines expressing empty vector control (MEF^la/vec), hAPE1 (MEF^la/hAPE1), and mApe1 (MEF^la/mApe1). Three batches of total RNA were prepared (Qiagen RAeasy) from each cell line. The qualities of RNA were verified by Agilent 2100 Bioanalyzer (Agilent Technology) and then the set of nine RNA samples (three preparations from three cell lines) were analyzed using GeneChip FLUIDICS station 450 and Affymetrix GeneChip Scanner 7G (Affymetrix) at the Microarray Core of the University of Kentucky. Transcriptional intensities of 41,345 genes were processed using PARTEK, to obtain 7115 genes with false discovery rates less than 0.05. Genes of which expressions were over-represented in MEF^la/hAPE1 and MEF^la/mApe1 compared to MEF^la/vec were then calculated based on P values less than 0.001 (Fisher’s exact test) to obtain 557 and 766 genes for hAPE1 and mApe1, respectively. Functional annotations for these genes were then obtained using NCBI DAVID (Database for Annotation, Visualization and Integrated Discovery; http://david.abcc.ncifcrf.gov). The data will be available at NCBI Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE55765.

Suganya R., Chakraborty A., Miriyala S., Hazra T.K, & Izumi T. (2015). Suppression of oxidative phosphorylation in mouse embryonic fibroblast cells deficient in apurinic/apyrimidinic endonuclease. DNA repair, 27, 40-48.

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Transcriptional Profiling of A2EN Cells Infected with tepP Mutant

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Approximately 0.8×10⁶ A2EN cells were seeded per well in 6-well plates the day before experiment. Duplicate cell samples were mock infected, or infected with the tepP mutant strain transformed with empty vector or the vector harboring wild type tepP at an MOI of 10. Infections were synchronized by centrifugation at 3000 rpm for 30 min at 10°C, followed by an immediate shift to 37°C with pre-warmed cell culture media. Samples were collected at 4 hpi using QIAGEN RNeasy Plus Mini Kit (QIAGEN, Valencia, CA, USA) as described by the manufacturer. RNA integrity was assessed with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA, USA) and quantified with a Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE, USA). Hybridization targets were prepared with MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX, USA) from total RNA, hybridized to GeneChip Human Genome U133A 2.0 arrays in Affymetrix GeneChip hybridization oven 645, washed in Affymetrix GeneChip Fluidics Station 450 and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara, CA, USA). Data analysis was performed using Partek Genomic Suite 6.6 (Partek Inc., Saint Louis, MO, USA).

Chen Y.S., Bastidas R.J., Saka H.A., Carpenter V.K., Richards K.L., Plano G.V, & Valdivia R.H. (2014). The Chlamydia trachomatis Type III Secretion Chaperone Slc1 Engages Multiple Early Effectors, Including TepP, a Tyrosine-phosphorylated Protein Required for the Recruitment of CrkI-II to Nascent Inclusions and Innate Immune Signaling. PLoS Pathogens, 10(2), e1003954.

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Affymetrix GeneChip Hybridization and Staining

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The samples were randomized into hybridization groups, each containing members from all 3 previous amplification groups and each processed as a unit. The GeneChip Hybridization, Wash & Stain Kit (Affymetrix, Thermo Fisher Scientific Inc.) contained all the necessary reagents. The Hybridization Module of the kit supplied controls and master mix that was combined with the fragmented, labeled ssDNA, and added to pre-warmed Affymetrix GeneChip HuGene 2.0 ST Array, Format 100, chips for hybridization overnight. The Stain Module of the kit provided high-stringency wash solutions to be used in the Affymetrix GeneChip Fluidics Station 450. After washing, the array chips were scanned on the Affymetrix GeneChip Scanner 7G.

Booth J.L., Duggan E.S., Patel V.I., Wu W., Burian D.M., Hutchings D.C., White V.L., Coggeshall K.M., Dozmorov M.G, & Metcalf J.P. (2018). Gene Expression Profiling of Primary Human Type I Alveolar Epithelial Cells Exposed to Bacillus anthracis Spores Reveals Induction of Neutrophil and Monocyte Chemokines. Microbial pathogenesis, 121, 9-21.

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