RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis
Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimat...
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| Published in | BioTechniques Vol. 59; no. 6; pp. 347 - 358 |
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| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Future Science Ltd
01.12.2015
Eaton Publishing Taylor & Francis Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips. |
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| AbstractList | Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips. Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips. |
| Author | Demanèche, Sandrine Simonet, Pascal Navarro, Elisabeth Reboulet, Jérémy Scorretti, Riccardo Fabrègue, Olivier Dawson, Lorna |
| AuthorAffiliation | 2IRD-UMR LSTM, Campus de Baillarguet, Montpellier, France 3James Hutton Institute, Aberdeen, UK 1Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France |
| AuthorAffiliation_xml | – name: 2IRD-UMR LSTM, Campus de Baillarguet, Montpellier, France – name: 3James Hutton Institute, Aberdeen, UK – name: 1Université de Lyon, Laboratoire Ampère (CNRS UMR5005), Environmental Microbial Genomics, École Centrale de Lyon, Ecully, France |
| Author_xml | – sequence: 1 givenname: Elisabeth surname: Navarro fullname: Navarro, Elisabeth – sequence: 2 givenname: Olivier surname: Fabrègue fullname: Fabrègue, Olivier – sequence: 3 givenname: Riccardo surname: Scorretti fullname: Scorretti, Riccardo – sequence: 4 givenname: Jérémy surname: Reboulet fullname: Reboulet, Jérémy – sequence: 5 givenname: Pascal surname: Simonet fullname: Simonet, Pascal – sequence: 6 givenname: Lorna surname: Dawson fullname: Dawson, Lorna – sequence: 7 givenname: Sandrine surname: Demanèche fullname: Demanèche, Sandrine |
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| SubjectTerms | Algorithms alignment tool DNA Fingerprinting - methods DNA, Intergenic - chemistry Electric power Engineering Sciences microbial ecology Nonlinear Dynamics Principal Component Analysis RISA comparison Software Soil Microbiology |
| Title | RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis |
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