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Journal article
Development and Validation of an Haemophilus influenzae Supragenome Hybridization (SGH) Array for Transcriptomic Analyses
PloS one, v 9(10), pp e105493-e105493
07 Oct 2014
PMCID: PMC4188559
PMID: 25290153
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
We previously carried out the design and testing of a custom-built Haemophilus influenzae supragenome hybridization (SGH) array that contains probe sequences to 2,890 gene clusters identified by whole genome sequencing of 24 strains of H. influenzae. The array was originally designed as a tool to interrogate the gene content of large numbers of clinical isolates without the need for sequencing, however, the data obtained is quantitative and is thus suitable for transcriptomic analyses. In the current study RNA was extracted from H. influenzae strain CZ4126/02 (which was not included in the design of the array) converted to cDNA, and labelled and hybridized to the SGH arrays to assess the quality and reproducibility of data obtained from these custom-designed chips to serve as a tool for transcriptomics. Three types of experimental replicates were analyzed with all showing very high degrees of correlation, thus validating both the array and the methods used for RNA profiling. A custom filtering pipeline for two-condition unpaired data using five metrics was developed to minimize variability within replicates and to maximize the identification of the most significant true transcriptional differences between two samples. These methods can be extended to transcriptional analysis of other bacterial species utilizing supragenome-based arrays.
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Details
- Title
- Development and Validation of an Haemophilus influenzae Supragenome Hybridization (SGH) Array for Transcriptomic Analyses
- Creators
- Benjamin A. Janto - Drexel UniversityN. Luisa Hiller - Carnegie Mellon UniversityRory A. Eutsey - Allegheny-Singer Research InstituteMargaret E. Dahlgren - Allegheny-Singer Research InstituteJoshua P. Earl - Allegheny-Singer Research InstituteEvan Powell - Allegheny-Singer Research InstituteAzad Ahmed - Allegheny-Singer Research InstituteFen Z. Hu - Drexel UniversityGarth D. Ehrlich - Drexel University
- Publication Details
- PloS one, v 9(10), pp e105493-e105493
- Publisher
- Public Library Science
- Number of pages
- 11
- Grant note
- DC002148; DC02148 - 16S1; AI080935 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA R01DC002148 / NATIONAL INSTITUTE ON DEAFNESS AND OTHER COMMUNICATION DISORDERS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute on Deafness & Other Communication Disorders (NIDCD) Allegheny General Hospital; General Electric R01AI080935 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) Allegheny-Singer Research Institute
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology
- Web of Science ID
- WOS:000342798000003
- Scopus ID
- 2-s2.0-84907789929
- Other Identifier
- 991019168806904721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Microbiology