DNCT+ cells were cultured for 2 d with or without Dox, and then total RNA was prepared using TRIzol Reagent (Life Technologies Japan, Tokyo, Japan) and purified using the SV Total RNA Isolation System (Promega KK, Tokyo, Japan). cRNA was amplified and labeled using a Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and hybridized to a 44 K Agilent 60-mer oligomicroarray (Canine Oligo Microarray Kit; Agilent Technologies). 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).
Agilent feature extraction software version 9.5.1.1
Manufactured by Agilent Technologies
Agilent Feature Extraction Software (version 9.5.1.1) is a software tool used for processing and analyzing data from microarray experiments. The software is designed to automatically extract quantitative information from microarray image files, including feature intensities and background signals.
Automatically generated - may contain errors
Lab products found in correlation
4 protocols using agilent feature extraction software version 9.5.1.1
1
Canine Gene Expression Profiling
2
Transcriptome Analysis of MDCK Cell Subpopulations
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Total RNA was prepared from DsRed+, DECT+, Snail+ MDCK cells using TRIzol Reagent (Invitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions. cRNA was amplified and labelled using a Quick Amp Labelling Kit (Agilent Technologies) and hybridized to a 44 K Agilent 60-mer oligomicroarray (Canine Oligo Microarray Kit; 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 Agilent Feature Extraction Software (version 9.5.1.1). Microarray data analysis was supported by Cell Innovator (Fukuoka, Japan).
3
RNA Extraction and Microarray Analysis
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Total RNA was prepared from DsRed+, and Snail+ DLD-1 cells using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and purified as previously described [12] (link). cRNA was amplified and labeled using a Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and hybridized to a 44 K Agilent 60-mer oligomicroarray (Human Oligo Microarray Kit). 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).
4
Transcriptome Analysis of Fibroblasts
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DNA microarray analysis was performed using SurePrint G3 Human Gene Expression Microarrays 8 Â 60 K version 2 (Agilent Technologies). In brief, total RNA from fibroblasts maintained in DMEM with 10% FBS was prepared with the RNeasy Mini Kit. Relative target intensity was calculated using Agilent Feature Extraction Software version 9.5.1.1 (Agilent Technologies). The data were deposited at the National Center for Biotechnology Information (https://www. ncbi.nlm.nih.gov/geo; accession number GSE99007). We generated a heat map using MeV software version 4.8.1 (Multiple Experiment Viewer; http://www.tm4.org) and a hierarchical clustering method to sort the genes. Gene Set Enrichment Analysis (http://www.broadinstitute.org/gsea/ index.jsp) of the expression data was used to assess enrichment of the up-regulated genes from GSE40839 26 and GSE63659. 27
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