ArticleBMC genomics2005
Increased DNA microarray hybridization specificity using sscDNA targets.
Article in BMC genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 38 citations in OpenAlex.
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- Infragranular gene expression disturbances in the prefrontal cortex in schizophrenia: signature of altered neural development?Neurobiology of disease · 2010Article
- Triptolide induces anti-inflammatory cellular responses.American journal of translational research · 2009Article
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- Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray.Biomarker insights · 2008Article
- Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system.BMC genomics · 2008Article
- Disease-specific gene expression profiling in multiple models of lung disease.American journal of respiratory and critical care medicine · 2008Article
- Comparison of RNA amplification techniques meeting the demands for the expression profiling of clinical cancer samples.Virchows Archiv : an international journal of pathology · 2007Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThe most widely used amplification method for microarray analysis of gene expression uses T7 RNA polymerase-driven in vitro transcription (IVT) to produce complementary RNA (cRNA) that can be hybridized to arrays. However, multiple rounds of amplification are required when assaying very small amounts of starting RNA. Moreover, certain cRNA-DNA mismatches are more stable than the analogous cDNA-DNA mismatches and this might increase non-specific hybridization. We sought to determine whether a recently developed linear isothermal amplification method (ribo-SPIA) that produces single stranded cDNA would offer advantages over traditional IVT-based methods for microarray-based analyses of transcript expression.
resultsA single round of ribo-SPIA amplification produced sufficient sscDNA for hybridizations when as little as 5 ng of starting total RNA was used. Comparisons of probe set signal intensities obtained from replicate amplifications showed consistently high correlations (r = 0.99). We compared gene expression in two different human RNA samples using ribo-SPIA. Compared with one round IVT, ribo-SPIA had a larger dynamic range and correlated better with quantitative PCR results even though we used 1000-fold less starting RNA. The improved dynamic range was associated with decreases in hybridization to mismatch control probes.
conclusionThe use of amplified sscDNA may offer substantial advantages over IVT-based amplification methods, especially when very limited amounts of starting RNA are available. The use of sscDNA targets instead of cRNA targets appears to improve hybridization specificity.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.