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2. Additional file 4 of Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Author

Jackson, Scott A, Isha R Patel, Barnaba, Tammy, LeClerc, Joseph E, and Cebula, Thomas A

Subjects
fungi
Abstract

Additional File 4:Conserved, core, backbone genes in E. coli and Shigella. Using the MAS 5.0 gene detection method, we filtered those probe sets that were called "present" in all 207 isolates. The 2256 conserved probe sets are listed here along with their gene description, when available. (PDF 77 KB)

Published
2020
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4. Additional file 2 of Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Author

Jackson, Scott A, Isha R Patel, Barnaba, Tammy, LeClerc, Joseph E, and Cebula, Thomas A

Abstract

Additional File 2:Pearson correlation matrix. R-Bioconductor was used to calculate Pearson correlation coefficients using RMA-summarized probe set intensities. The cells are color-coded to show relatedness and correlation (coefficient from 0-1) according to the scale below. Strains are ordered based on their relatedness as determined by hierarchical cluster analysis. (PDF 593 KB)

Published
2020
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5. Additional file 3 of Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Author

Jackson, Scott A, Isha R Patel, Barnaba, Tammy, LeClerc, Joseph E, and Cebula, Thomas A

Abstract

Additional File 3:Hierarchical Cluster Analysis. RMA-summarized probe set intensities were used to hierarchically cluster (Euclidean means) all 207 isolates (top dendrogram) and all 10,208 genes (left dendrogram) in Spotfire. The heatmap shows RMA probe set intensities from low (green) to high (red). The top dendrogram is color-coded based on the 3 large clusters of E. coli. (PDF 4 MB)

Published
2020
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6. Additional file 5 of Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Author

Jackson, Scott A, Isha R Patel, Barnaba, Tammy, LeClerc, Joseph E, and Cebula, Thomas A

Abstract

Additional File 5:Conserved Intergenic Regions. Using the MAS 5.0 gene detection method, we filtered those probe sets that were annotated as "intergenic" and called "present" in all 207 isolates. The 232 conserved intergenic probe sets are listed here along with their genome position and length. (PDF 17 KB)

Published
2020
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7. Additional file of Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Author

Jackson, Scott A, Isha R Patel, Barnaba, Tammy, LeClerc, Joseph E, and Cebula, Thomas A

Subjects
human activities
Abstract

Additional file of Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Published
2020
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8. Additional file 1 of Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Author

Jackson, Scott A, Isha R Patel, Barnaba, Tammy, LeClerc, Joseph E, and Cebula, Thomas A

Abstract

Additional File 1:Gene differences matrix. Number of gene differences based on strain-to-strain comparisons is shown. A "gene difference" is defined here as a 4-fold difference in the RMA-summarized probe set intensities. The cells are color-coded based on the number of gene differences using the scale below. Strains are ordered based on their relatedness as determined by hierarchical cluster analysis. (PDF 613 KB)

Published
2020
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12. Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Author

LeClerc Joseph E, Barnaba Tammy, Patel Isha R, Jackson Scott A, and Cebula Thomas A

Subjects
genome, diversity, microarray, Escherichia coli, Shigella, O157:H7, gene content, pathogenic determinants, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The gene content of a diverse group of 183 unique Escherichia coli and Shigella isolates was determined using the Affymetrix GeneChip® E. coli Genome 2.0 Array, originally designed for transcriptome analysis, as a genotyping tool. The probe set design utilized by this array provided the opportunity to determine the gene content of each strain very accurately and reliably. This array constitutes 10,112 independent genes representing four individual E. coli genomes, therefore providing the ability to survey genes of several different pathogen types. The entire ECOR collection, 80 EHEC-like isolates, and a diverse set of isolates from our FDA strain repository were included in our analysis. Results From this study we were able to define sets of genes that correspond to, and therefore define, the EHEC pathogen type. Furthermore, our sampling of 63 unique strains of O157:H7 showed the ability of this array to discriminate between closely related strains. We found that individual strains of O157:H7 differed, on average, by 197 probe sets. Finally, we describe an analysis method that utilizes the power of the probe sets to determine accurately the presence/absence of each gene represented on this array. Conclusions These elements provide insights into understanding the microbial diversity that exists within extant E. coli populations. Moreover, these data demonstrate that this novel microarray-based analysis is a powerful tool in the field of molecular epidemiology and the newly emerging field of microbial forensics.

Published
2011
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13. Quality sample collection, handling, and preservation for an effective microbial forensics program

Author

Budowle, Bruce, Valentine, Nancy B., Yadev, Jagjit, Schutzer, Steven E., Rodriguez, Luis L., Morse, Stephen A., McKenna, Thomas S., Marrone, Babetta L., Burnas, James P., Keller, Frederick Paul, Kuske, Cheryl, Leclerc, Joseph E., Beecher, Douglas, J., Hale, Martha L., Harris, Robert B., Fletcher, Jacqueline, Chakraborty, Ranajit, and Cebula, Thomas A.

Subjects
Forensic sciences -- Conferences, meetings and seminars, Microbiology -- Conferences, meetings and seminars, Biological sciences
Abstract

A series of meetings were held at the Banbury Center, Cold Spring harbor, NY to address specific issues for the enhancement of microbial forensic capability. The microbial forensic investigation and its success is dependent upon proper collection, handling and preservation of sample or physical evidence, therefore, efforts should be intensified in these areas to ensure capability for robust development, validation and reliability of microbial forensics to support the attribution of crimes.

Published
2006

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