Resources
Protocols
Metatranscriptomics of the human oral microbiome during health and disease
Peter Jorth, Keith Turner, Pinar Gumus, Nejat Nizam, Nurcan Buduneli, Marvin Whiteley
The following excel files support the above named manuscript.
Supplementary file 1.Metagenome information. Phylogeny of represented genomes is shown from Kingdom to the Species level for samples from patients 1, 2, and 3. Representative genomes are indicated. 16S sequencing names marked in blue are represented by genomes from closely related organisms, while those in red represent perfect matches. The phylogenetic match level for each representative genome is also indicated. The name of the representative genome is shown followed by its source, Genbank or HOMD. Mean prevalence of each identified 16S sequence during health and disease is also shown.
Supplementary file 2.Differential expression analysis of the 60-species metagenome. Expression analysis results from paired edgeR analyses are shown. The log2 fold-change during disease for each genetic locus is shown, followed by the mean log2 read counts per million reads, and the P-value determined by edgeR. Gene product descriptions, EC numbers, and metabolic pathways are provided for each gene when available.
Supplementary file 3.Differential expression analysis by EC enzyme-coding genes. Expression analysis results from paired edgeR analyses are shown. Raw read counts per EC per sample are shown. The log2 fold-change during disease for each EC is shown, followed by the mean log2 read counts per million reads, and the P-value determined by edgeR.
A. actinomycetemcomitans RNA-seq Annotation Files
The following supports Jorth et al. (2013). Probing bacterial metabolism during infection using high-resolution transcriptomics. J Bacteriol. 195: 4991-4998.
RNA-seq annotation files including non-coding RNAs and transcriptional start sites are provided in genbank and gff formats. Genbank files are easily opened with many nucleic acid sequence viewers including CLC Sequence viewer. The gff files can be used for RNA-seq analyses using HT-Seq and IGV.
Microbiology Information
Pseudomonas genome web page
Pseudomonas mutant library
Aa genome web page
Biofilm information
Quorum Sensing information
Funding Links
Cystic Fibrosis Foundation
NIH
NIH Ruth L. Kirschstein NRSA pre-doctoral fellowship
NSF
Burroughs Wellcome
USDA
