ArticleAmerican journal of physiology. Cell physiology2005
Microarray-based comparison of three amplification methods for nanogram amounts of total RNA.
Article in American journal of physiology. Cell physiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 74 citations in OpenAlex.
- Combined use of laser capture microdissection and cDNA microarray analysis identifies locally expressed disease-related genes in focal regions of psoriasis vulgaris skin lesions.The Journal of investigative dermatology · 2012Trial
- LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue.Heliyon · 2024Article
- The footprint of the ageing stroma in older patients with breast cancer.Breast cancer research : BCR · 2017Article
- Selective gene expression analysis of the neuroepithelial body microenvironment in postnatal lungs with special interest for potential stem cell characteristics.Respiratory research · 2017Article
- Laser capture microdissection: Big data from small samples.Histology and histopathology · 2015Review
- Transcriptional analysis of micro-dissected articular cartilage in post-traumatic murine osteoarthritis.Osteoarthritis and cartilage · 2015Article
- Stem Cell Strategies to Evaluate Idiosyncratic Drug-induced Liver Injury.Journal of clinical and translational hepatology · 2014Review
- Slc26a7 chloride channel activity and localization in mouse Reissner's membrane epithelium.PloS one · 2014Article
- Gene expression analyses of mouse aortic endothelium in response to atherogenic stimuli.Arteriosclerosis, thrombosis, and vascular biology · 2013Article
- Establishment of a protocol for large-scale gene expression analyses of laser capture microdissected bladder tissue.World journal of urology · 2012Article
- Influence of RNA labeling on expression profiling of microRNAs.The Journal of molecular diagnostics : JMD · 2012Article
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- Global array-based transcriptomics from minimal input RNA utilising an optimal RNA isolation process combined with SPIA cDNA probes.PloS one · 2011Article
- Clinical microfluidics for neutrophil genomics and proteomics.Nature medicine · 2010Article
- Cell-specific gene expression in Langerhans cell histiocytosis lesions reveals a distinct profile compared with epidermal Langerhans cells.Journal of immunology (Baltimore, Md. : 1950) · 2010Article
- Collection of epithelial cells from rodent mammary gland via laser capture microdissection yielding high-quality RNA suitable for microarray analysis.Biological procedures online · 2010Article
- Detection call algorithms for high-throughput gene expression microarray data.Briefings in bioinformatics · 2010Review
- Developmental delays consistent with cochlear hypothyroidism contribute to failure to develop hearing in mice lacking Slc26a4/pendrin expression.American journal of physiology. Renal physiology · 2009Article
- Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Gene expression profiling using microarrays requires microgram amounts of RNA, which limits its direct application for the study of nanogram RNA samples obtained using microdissection, laser capture microscopy, or needle biopsy. A novel system based on Ribo-SPIA technology (RS, Ovation-Biotin amplification and labeling system) was recently introduced. The utility of the RS system, an optimized prototype system for picogram RNA samples (pRS), and two T7-based systems involving one or two rounds of amplification (One RA, Standard Protocol, or Two RA, Small Sample Prototcol, version II) were evaluated in the present study. Mouse kidney (MK) and mouse universal reference (MUR) RNA samples, 0.3 ng to 10 mug, were analyzed using high-density Affymetrix Mouse Genome 430 2.0 GeneChip arrays. Call concordance between replicates, correlations of signal intensity, signal intensity ratios, and minimal fold increase necessary for significance were determined. All systems amplified partially overlapping sets of genes with similar signal intensity correlations. pRS amplified the highest number of genes from 10-ng RNA samples. We detected 24 of 26 genes verified by RT-PCR in samples prepared using pRS. Two RA yielded somewhat higher call concordances than did RS and pRS (91.8% vs. 89.3% and 88.1%, respectively). Although all target preparation methods were suitable, pRS amplified the highest number of targets and was found to be suitable for amplification of as little as 0.3 ng of total RNA. In addition, RS and pRS were faster and simpler to use than the T7-based methods and resulted in the generation of cDNA, which is more stable than cRNA.
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Registered trials
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.