Transcriptomics

Dataset Information

3

Microarray analysis of microbiota of gingival lesions in noma patients


ABSTRACT: We used phylogenetic low-density microarrays targeting the 16S rRNA gene to characterize the gingival flora of acute noma and acute necrotizing gingivitis lesions, and compared them to healthy control subjects of the same geographical and social background. Various types of samples were collected (column characteristics); patients from the same hospital without mouth infection (H), matched control populations (T), patients suffering gengivitis (Gengivitis), patient suffering NOMA (noma), patient suffering NOMA receiving antimicrobials (N-ATB). Sampled from patients were retrieved from both sides (column Description); healthy- or lesion-side of the mouth. All controls are matched with specific patients (see column patient category and number) We designed low-density 16S rDNA arrays representing 339 different phylotypes. We used an arbitrary cutoff of 1% of overall abundance to select from this dataset the most abundant sequences for probe design. Using this cutoff, the 132 most abundant 16S rRNA gene sequences were scanned for probes respecting defined physico-chemical properties (Tm = 65±5°C; probe length = 23–50 nt; < -5.0 kcal/mol for hairpins; < -8.0 kcal/mol for self-dimers; and dinucleotide repeats shorter than 5 bp) using a commercial software (Array Designer TM 2.0 by Premier Biosoft). The 335 oligonucleotide probes were synthesized with a C6-linker with free primary amine (Sigma-Aldrich) and spotted on ArrayStrips microarrays (Clondiag GmbH, Jena, Germany).

ORGANISM(S): human oral metagenome  

SUBMITTER: Antoine Huyghe   Ignacio Bolivar  Patrice François  FRANCOIS Patrice  Didier Pittet 

PROVIDER: E-GEOD-43612 | ArrayExpress | 2013-12-27

SECONDARY ACCESSION(S): GSE43612PRJNA186823

REPOSITORIES: GEO, ArrayExpress

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Publications

Microarray analysis of microbiota of gingival lesions in noma patients.

Huyghe Antoine A   François Patrice P   Mombelli Andrea A   Tangomo Manuela M   Girard Myriam M   Baratti-Mayer Denise D   Bolivar Ignacio I   Pittet Didier D   Schrenzel Jacques J  

PLoS neglected tropical diseases 20130926 9


Noma (cancrum oris) is a gangrenous disease of unknown etiology affecting the maxillo-facial region of young children in extremely limited resource countries. In an attempt to better understand the microbiological events occurring during this disease, we used phylogenetic and low-density microarrays targeting the 16S rRNA gene to characterize the gingival flora of acute noma and acute necrotizing gingivitis (ANG) lesions, and compared them to healthy control subjects of the same geographical and  ...[more]

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