Agilent human gene expression microarrays were performed and analyzed as previously described (Xie et al., 2018 (link)). Briefly, total RNA was extracted by using the Trizol (Thermo Fisher Scientific) method and applied to the Agilent human GE 4× 44K v2 microarrays (G4845A) according to the manufacturer’s protocol. Raw data was extracted using Agilent Feature Extraction 9.5.3.1 software and was preprocessed and normalized by R statistical software. The Bioconductor limma package and Loess and Aquantile normalization were performed for within-array and between-arrays normalization. Median of the M values (M value = log2 [Treated/Mock]) for individual gene was computed from multiple probes that reside within the same gene. Genes with median M value ≥ 1 were considered as upregulated with respect to Mock cells, whereas genes with median M value ≤ −1 were marked as downregulated genes in this study.
Agilent human gene expression microarrays
Manufactured by Agilent Technologies
Sourced in United States
Agilent human gene expression microarrays are a tool for analyzing the expression levels of thousands of human genes simultaneously. The microarrays contain probes that can detect and measure the abundance of specific RNA molecules, providing comprehensive insights into the transcriptional activity of the human genome.
Automatically generated - may contain errors
Lab products found in correlation
Trizol reagent, by Thermo Fisher Scientific (2 mentions)
Trizol, by Thermo Fisher Scientific (1 mentions)
Agilent human ge 4 44 k v2 microarrays, by Agilent Technologies (1 mentions)
Nanodrop nd 2000 spectrophotometer, by Thermo Fisher Scientific (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Agilent scanner g2505c, by Agilent Technologies (1 mentions)
Metacore, by Thomson Reuters (1 mentions)
3 protocols using agilent human gene expression microarrays
1
Microarray Analysis of Gene Expression
2
Transcriptome Analysis of Renal Cell Carcinoma
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For total RNA extraction, NC/786-O and B7-H4/786-O cells were harvested. Triplicate samples were prepared for each cell line. Total RNA was extracted using TRIzol reagent (Invitrogen, Thermo Fisher Scientific, Inc.) according to the manufacturer's protocol. Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies; Thermo Fisher Scientific, Inc.) and the RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc.). Total RNA was transcribed into double-stranded cDNA and labeled with cyanine-3-cytidine triphosphate. The labeled cDNAs were hybridized onto Agilent Human Gene Expression microarrays (Agilent Technologies, Inc.). The arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies, Inc.). The heatmap of the gene expression in the two cell lines (triplicates of each cell line) was produced by Multiexperimental Viewer software version 4.8.1 (MeV development team).
3
Transcriptomic Analysis of Breast Cancer Cells
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Total RNA was extracted from three independent passages of 70 % confluent cells for each of the four cell lines (MCF-7 parental, MCF-7acq, MDA-MB-231 parental and MDAacq) using Trizol reagent (Invitrogen). Expression analysis using Agilent Human Gene Expression Microarrays (G4845A, Agilent Techologies, Santa Clara, CA, USA), image quality, background correction and normalization were conducted as previously described [22 (link)]. Sample clustering was performed by the ‘ward’ method in the software R (http://www.r-project.org/ ). Statistical tests were performed using a moderated t-test, and p-values were adjusted for multiple testing by the Benjamin & Hochberg method [23 ]. Genes were considered significantly differentially expressed if the adjusted p-value < 0.05 and the absolute log2-fold change > 0.8. Gene Set Enrichment Analysis (GSEA) was performed using the Clusterprofiler package [24 (link)] using Reactome, KEGG and the GeneOntology data distributed Bioconductor project. Network analysis was performed using MetaCore from Thomson Reuters. Networks were constructed based on direct interactions in the MetaCore database for all deregulated genes with a log2 fold change > 1 and p-value < 0.05. For each cell line three biological replicates were analyzed.
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