Title |
RNA quality in frozen breast cancer samples and the influence on gene expression analysis – a comparison of three evaluation methods using microcapillary electrophoresis traces
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Published in |
BMC Molecular and Cell Biology, May 2007
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DOI | 10.1186/1471-2199-8-38 |
Pubmed ID | |
Authors |
Carina Strand, Johan Enell, Ingrid Hedenfalk, Mårten Fernö |
Abstract |
Assessing RNA quality is essential for gene expression analysis, as the inclusion of degraded samples may influence the interpretation of expression levels in relation to biological and/or clinical parameters. RNA quality can be analyzed by agarose gel electrophoresis, UV spectrophotometer, or microcapillary electrophoresis traces, and can furthermore be evaluated using different methods. No generally accepted recommendations exist for which technique or evaluation method is the best choice. The aim of the present study was to use microcapillary electrophoresis traces from the Bioanalyzer to compare three methods for evaluating RNA quality in 24 fresh frozen invasive breast cancer tissues: 1) Manual method = subjective evaluation of the electropherogram, 2) Ratio Method = the ratio between the 28S and 18S peaks, and 3) RNA integrity number (RIN) method = objective evaluation of the electropherogram. The results were also related to gene expression profiling analyses using 27K oligonucleotide microarrays, unsupervised hierarchical clustering analysis and ontological mapping. |
X Demographics
Geographical breakdown
Country | Count | As % |
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Unknown | 1 | 100% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 1 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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United Kingdom | 3 | 3% |
Germany | 1 | 1% |
Malaysia | 1 | 1% |
Brazil | 1 | 1% |
Australia | 1 | 1% |
Japan | 1 | 1% |
United States | 1 | 1% |
Unknown | 77 | 90% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 23 | 27% |
Student > Ph. D. Student | 18 | 21% |
Student > Master | 9 | 10% |
Student > Bachelor | 7 | 8% |
Student > Postgraduate | 5 | 6% |
Other | 14 | 16% |
Unknown | 10 | 12% |
Readers by discipline | Count | As % |
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Agricultural and Biological Sciences | 36 | 42% |
Medicine and Dentistry | 15 | 17% |
Biochemistry, Genetics and Molecular Biology | 11 | 13% |
Engineering | 4 | 5% |
Chemistry | 3 | 3% |
Other | 3 | 3% |
Unknown | 14 | 16% |