Double-stranded cDNA was synthesized from 100 ng of total RNA with the GeneAtlas 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). Biotin-labeled amplified RNA (aRNA) was synthesized by in vitro transcription using the GeneChip 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). A total of 9.4 mg of purified aRNA was fragmented using the GeneAtlas 3’ IVT Express Kit and was hybridized for 16 h at 45°C using GeneChip MG-430 PM microarray (Affymetrix Inc., Santa Clara, CA, USA). The chip was washed and stained in the Gene Atlas Fluidics Station 400 (Affymetrix Inc., Santa Clara, CA, USA) and then the resulting image was scanned using the GeneAtlas Imaging Station (Affymetrix Inc., Santa Clara, CA, USA). Data analysis was performed using the Partek Express software (Partek Inc., St. Louis, MO, USA) provided by Affymetrix as part of their GeneAtlas system. Compared with the non-treated cells, fold change in expression in the TCQA-treated group was calculated and converted to log 2 data.
Gene atlas fluidics station 400
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Gene Atlas Fluidics Station 400 is a laboratory instrument designed for automated sample preparation and processing. It is capable of performing various fluidic operations, such as liquid handling, reagent dispensing, and sample mixing, to facilitate genetic analysis workflows. The core function of the Gene Atlas Fluidics Station 400 is to provide a standardized and reproducible platform for sample preparation in life science research applications.
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Lab products found in correlation
Geneatlas imaging station, by Thermo Fisher Scientific (8 mentions)
Geneatlas 3 ivt express kit, by Thermo Fisher Scientific (5 mentions)
Genechip 3 ivt express kit, by Thermo Fisher Scientific (4 mentions)
Genechip mg 430 pm microarray, by Thermo Fisher Scientific (3 mentions)
Partek express software, by Thermo Fisher Scientific (1 mentions)
Pathway studio explore 1, by Thermo Fisher Scientific (1 mentions)
Affymetrix expression console software, by Thermo Fisher Scientific (1 mentions)
Genechip mouse genome 430 2.0 array, by Thermo Fisher Scientific (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Isogen solution, by Nippon Gene (1 mentions)
Genechip 3 ivt plus reagent kit, by Thermo Fisher Scientific (1 mentions)
8 protocols using gene atlas fluidics station 400
1
Microarray Gene Expression Analysis
2
Limbic Brain Transcriptome Analysis
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DNA microarray analysis was conducted on isolated RNAs extracted from the limbic area of mice brains as reported previously [10 (link)]. Double-stranded cDNA was synthesized from 100 ng of total RNA with the GeneAtlas 3´ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). Biotin-labeled amplified RNA (aRNA) was synthesized by in vitro transcription using the GeneChip 3´ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). Briefly, purified aRNA was fragmented using the GeneAtlas 3´ IVT Express Kit and hybridized for 16 h at 45°C using the GeneChip MG-430 PM microarray (Affymetrix Inc., Santa Clara, CA, USA). The chip was washed and stained in the Gene Atlas Fluidics Station 400 (Affymetrix Inc., Santa Clara, CA, USA), and the resulting image was scanned using the GeneAtlas Imaging Station (Affymetrix Inc., Santa Clara, CA, USA). Data analysis was performed using the Affymetrix Expression Console Software version and Visualization and Integrated Discovery (DAVID) software version 6.8 (National Institute of Allergy and Infectious Diseases (NIAID). Compared with the control (vehicle-treated group), fold-changes in the expression of genes in the imipramine- or EEA-treated groups were calculated and converted to linear data.
3
Affymetrix HG-U219 Microarray Analysis
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Microarray hybridization probes were generated from isolated RNA samples. Double-stranded cDNA was synthesized from 100 ng of total RNA using the GeneAtlas 3′ IVT Express Kit (Affymetrix, Inc.). Biotin-labeled aRNA was synthesized by in vitro transcription and purified. 10 μg of purified aRNA was then fragmented using the GeneAtlas 3′ IVT Express Kit and was hybridized to the Affymetrix HG-U219 (Affymetrix) for 16 h at 45°C. The chips were washed and stained in the GeneAtlas Fluidics Station 400 (Affymetrix) and then imaged in the GeneAtlas Imaging Station (Affymetrix). The Partek Express software (Affymetrix) served for the data analysis by running comparisons of gene expression in treated and control cells based on mathematical algorithms. The generated data (significant fold change in gene expression) was then analyzed using the Pathway Studio Explore 1.1 software (Affymetrix).
4
Affymetrix GeneChip Transcriptome Analysis
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DNA microarray was performed using Affymetrix (Santa Clara, CA, USA) GeneChip Mouse Genome 430 2.0 Array following the manufacturer’s instructions. Total RNA was extracted from B16F10 cells (3 × 105 cells/ml) and the quality was assessed using Agilent 2100 bioanalyzer (Agilent Technologies). Biotin-labeled aRNA was synthesized by in vitro transcription and the purified aRNA (10 μg) was fragmented using the GeneAtlas 3’ IVT Express Kit, and was hybridized to the gene chip for 16 h at 45 °C. The chips were washed and stained in the GeneAtlas Fluidics Station 400 (Affymetrix) and the resulting image scanned using the GeneAtlas Imaging Station (Affymetrix). Identification of the differentially expressed genes was performed using Affymetrix® Expression Console™ Software and Affymetrix® Transcriptome Analysis Console (TAC) 2.0 Software (Affymetrix).
5
Microarray Gene Expression Analysis
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Template RNA was extracted using ISOGEN solution (Nippon Gene, Japan) as described above and was used to generate biotin-labeled aRNA and then purified and fragmented. The labeled and fragmented aRNA was subjected to hybridization using the GeneChip HG-U219 Array Strip Kit (Affymetrix, Santa Clara, CA, USA). The chip was washed and stained using the Gene Atlas Fluidics Station 400 and was scanned using the Gene Atlas Imaging Station (Affymetrix, Santa Clara, CA, USA). The resulting data were normalized using the Transcriptome Analysis Console (TAC) Software (version 4.0.1). Genes with fold change ≥ 1.5 (in linear space) and p-value ≤ 0.05 were considered differentially expressed genes (DEGs) and were used for further analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Visualization was partly conducted using R programming software.
6
Transcriptome Analysis via Affymetrix Microarray
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Firstly, 100 ng of total RNA was utilized to synthesize double-stranded cDNA, employing the GeneAtlas 3′ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). Subsequently, biotin-labeled amplified RNA (aRNA) was synthesized via in vitro transcription, employing the GeneChip 3′ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). Following purification, a total of 9.4 mg of aRNA was fragmented using the GeneAtlas 3′ IVT Express Kit. The fragmented aRNA was then subjected to a 16 h hybridization at 45 °C, utilizing the GeneChip MG-430 PM microarray chip (Affymetrix Inc., Santa Clara, CA, USA). After hybridization, the microarray chip was subjected to a series of washes and staining in the Gene Atlas Fluidics Station 400 (Affymetrix Inc., Santa Clara, CA, USA). Finally, the resulting image was scanned using the GeneAtlas Imaging Station (Affymetrix Inc., Santa Clara, CA, USA).
7
Gene Expression Analysis of EEB-Treated Brain
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DNA microarray analysis was conducted on isolated RNA samples from brains treated with EEB. DNA microarray analysis was performed as reported previously (Isoda et al., 2012 (link); Samet et al., 2015 (link)). Double-stranded cDNA was synthesized from 100 ng of total RNA with the GeneAtlas 3′ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). Biotin-labeled amplified RNA (aRNA) was synthesized by in vitro transcription using the GeneChip 3′ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA). A total of 9.4 mg of purified aRNA was fragmented using the GeneAtlas 3′ IVT Express Kit and was hybridized for 16 h at 45°C using GeneChip MG-430 PM microarray (Affymetrix Inc., Santa Clara, CA, USA). The chip was washed and stained in the Gene Atlas Fluidics Station 400 (Affymetrix Inc., Santa Clara, CA, USA) and then the resulting image was scanned using the GeneAtlas Imaging Station (Affymetrix Inc., Santa Clara, CA, USA). Data analysis was performed using the Partek Express software (Partek Inc., St. Louis, MO, USA) provided by Affymetrix as part of their GeneAtlas system. Compared with the control (water-treated group), fold change in expression in the imipramine- or EEB-treated group was calculated and converted to log 2 data.
8
Differential Gene Expression Analysis of NASH Model
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DNA microarray analysis was conducted on RNA samples isolated from liver tissue in the control group and novel NASH model group. Labeled cRNA was synthesized from 100 ng of total RNA using a GeneChip® 3’ IVT Plus Reagent Kit (Affymetrix, Inc., Santa Clara, CA, United States) according to the manufacturer’s protocol. Fragmented and labeled cRNA (7.5 μg) was hybridized to an Affymetrix Mouse MG-430 PM Array Strip (Affymetrix) for 16 h at 45 °C. The strips were washed and stained using a GeneAtlas Fluidics Station 400 (Affymetrix), and the resulting images were scanned using a GeneAtlas Imaging Station (Affymetrix). Probe-level analysis, including background subtraction and quantile normalization, was conducted using a robust multiarray average algorithm (RMA) using Affymetrix Expression Console Software 1.4 (Affymetrix). The gene expression profile of the novel NASH model was compared with the HF group. Genes exhibiting differences in expression with an increase of greater than 1.4-fold and a decrease of less than 0.65-fold were classified as differentially expressed genes[28 (link)].
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