The gene array assay was performed essentially as previously described (35 (link)). Briefly, total RNAs were extracted from formalin fixed paraffin embedded (FFPE) human lung cancer tissues. The integrity of the RNAs was examined by using the Agilent platform (2100 Bioanalyzer; Agilent Technologies, Palo Alto, CA). High quality total RNA was labeled using Illumina TotalPrep RNA Amplification kit from Ambion and hybridized on the Illumina Whole-Genome DASL Assay (HT-12 V4 Bead Chip platform) according to the manufacturer’s instructions. The studies were approved by the University of Pittsburgh Institutional Review Board (IRB).
Whole genome dasl assay ht 12 v4 bead chip platform
Manufactured by Illumina
The Whole-Genome DASL Assay (HT-12 V4 Bead Chip platform) is a gene expression profiling tool that utilizes bead-based technology to measure the expression levels of a large number of genes simultaneously. It is designed to provide a comprehensive analysis of the transcriptome from a variety of sample types, including formalin-fixed, paraffin-embedded (FFPE) tissues. The assay targets over 29,000 well-annotated genes, enabling a broad survey of the human genome.
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3 protocols using whole genome dasl assay ht 12 v4 bead chip platform
1
Transcriptome Profiling of FFPE Lung Cancer
2
Transcriptome Profiling of FFPE Lung Cancer
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The gene array assay was performed essentially as previously described (35 (link)). Briefly, total RNAs were extracted from formalin fixed paraffin embedded (FFPE) human lung cancer tissues. The integrity of the RNAs was examined by using the Agilent platform (2100 Bioanalyzer; Agilent Technologies, Palo Alto, CA). High quality total RNA was labeled using Illumina TotalPrep RNA Amplification kit from Ambion and hybridized on the Illumina Whole-Genome DASL Assay (HT-12 V4 Bead Chip platform) according to the manufacturer’s instructions. The studies were approved by the University of Pittsburgh Institutional Review Board (IRB).
3
Lung Cancer ERβ Expression Profile
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RNA was isolated using the High Pure FFPE RNA Isolation Kit (Roche) from FFPE sections from lung cancer cases that we have previously identified to have high ERβ (n = 15) and low ERβ (n = 49) protein expression by IHC [15 (link)]. The Illumina Whole-Genome DASL Assay (HT-12 V4 Bead Chip platform) was used to compare mRNA profiles between the ERβ high versus low expressing lung tumors. Data was analyzed using BeadStudio software and Biometric Research Branch (BRB) array tools Version 4.2.1 for subsequent analyses. The microarray data is available through ArrayExpress (accession number E-MTAB-3665).Validation of FGFR1 and FGFRL1 mRNA expression in the ERβ high/low cohort was performed using TaqMan q-RT-PCR and primer/probe sets from Invitrogen.
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