Ego, CA, USA), as previously described by Stranneheim et al. [18]. All sample preparation reagents were taken from the Illumina mRNA Sample Preparation Kit or ordered from vendors specified in the mRNA sample preparation protocol, except for automation specific reagents: carboxylic acid beads used for precipitation; the ethanol and tetraethylene glycol (EtOH/TEG) and the Polyethylene Glycol and sodium chloride (PEG/NaCl) precipitation buffers.Clustering and sequencingThe clustering of the bar-coded samples was performed on a cBot Cluster Generation System using an Illumina HiSeq Single Read Cluster Generation Kit according to the manufacturer’s instructions. The library preparations were sequenced on an Illumina HiSeq 2000 as single-reads to 100 bp. Two sequencing runs were performed according to the manufacturer’s instructions where two and three lanes were used in the first sequencing andGene Expression in PeriodontitisFigure 2. Expression of the inflammatory mediators in periodontitis-affected and healthy tissues obtained by RNA-seq. The bars show the expression (log2 fold change) pattern based on RNA-Seq reads of IL-1b, IL-6, IL-8, TNFa, RANTES and MCP-1. doi:10.1371/journal.pone.0046440.gsecond sequencing run, respectively (Table S1). The runs generated a total of 402 million reads with an average of 15 million reads per sample that passed the Illumina Chastity filter; these reads were included in the study.Sequence analysisAll sequences were aligned to the human genome reference hg19 with TopHat [19,20] version 1.1.4 and Samtools [21] version 0.1.8 using TopHat standard parameters except for parameters olexa1.3-quals -p 8 TF Homo_sapiens.GRCh37.59.gtf. Annotations from Ensembl and RefSeq, downloaded from University of California, Santa Cruz (UCSC) Genome Browser, were used to assign features to genomic positions. Sequences aligned to the human genome were assigned to features and counted using HTSeq 15755315 version 0.4.6 with parameters -m intersection-strict -s no -t exon. The R/Bioconductor package DESeq [22] was used to call differential 
gene expression on read counts generated by HTSeq and to perform hierarchical clustering of samples. All biological replicates for healthy and periodontitis-affected had R2 (Spearman) correlation of gene expression (read counts) above 0.92.Functional analyses of gene lists using WebGestaltFigure 3. Venn diagram of mRNA transcripts. Venn diagram showing genes that were uniquely expressed in periodontitis-affected (1375) and healthy (511) gingival tissues. The intersection of the two circles refers to transcripts, which are expressed in both periodontitisaffected and healthy gingival tissues (20 236). doi:10.1371/journal.pone.0046440.gAnalyses of gene categories and pathways was performed using the WEB-based Gene Set Analysis Toolkit v2 (WebGestalt) [23] with parameters: Id Type: Ensembl_gene_stable_id, Ref Set: Entrez Gene, Significance Level: p,0.05, Statistics Test: Hypergeometric, MTC: BH, Minimum: 2. KEGG analysis was used for pathway enrichment analysis and the Gene ontology (GO)Gene Expression in BIBS39 site PeriodontitisTable 2. Enriched regulated (KEGG) biological pathways among unique genes in periodontitis-affected tissues.Pathway Neuroactive ligand-receptor interaction Cytokine-cytokine receptor interaction Chemokine signaling pathway Intestinal immune network for IgA production Alanine, aspartate and glutamate metabolism Tyrosine metabolism Calcium signaling pathway Hedgehog signaling pathway 38916-34-6 web Systemic.Ego, CA, USA), as previously described by Stranneheim et al. [18]. All sample preparation reagents were taken from the Illumina mRNA Sample Preparation Kit or ordered from vendors specified in the mRNA sample preparation protocol, except for automation specific reagents: carboxylic acid beads used for precipitation; the ethanol and tetraethylene glycol (EtOH/TEG) and the Polyethylene Glycol and sodium chloride (PEG/NaCl) precipitation buffers.Clustering and sequencingThe clustering of the bar-coded samples was performed on a cBot Cluster Generation System using an Illumina HiSeq Single Read Cluster Generation Kit according to the manufacturer’s instructions. The library preparations were sequenced on an Illumina HiSeq 2000 as single-reads to 100 bp. Two sequencing runs were performed according to the manufacturer’s instructions where two and three lanes were used in the first sequencing andGene Expression in PeriodontitisFigure 2. Expression of the inflammatory mediators in periodontitis-affected and healthy tissues obtained by RNA-seq. The bars show the expression (log2 fold change) pattern based on RNA-Seq reads of IL-1b, IL-6, IL-8, TNFa, RANTES and MCP-1. doi:10.1371/journal.pone.0046440.gsecond sequencing run, respectively (Table S1). The runs generated a total of 402 million reads with an average of 15 million reads per sample that passed the Illumina Chastity filter; these reads were included in the study.Sequence analysisAll sequences were aligned to the human genome reference hg19 with TopHat [19,20] version 1.1.4 and Samtools [21] version 0.1.8 using TopHat standard parameters except for parameters olexa1.3-quals -p 8 TF Homo_sapiens.GRCh37.59.gtf. Annotations from Ensembl and RefSeq, downloaded from University of California, Santa Cruz (UCSC) Genome Browser, were used to assign features to genomic positions. Sequences aligned to the human genome were assigned to features and counted using HTSeq 15755315 version 0.4.6 with parameters -m intersection-strict -s no -t exon. The R/Bioconductor package DESeq [22] was used to call differential gene expression on read counts generated by HTSeq and to perform hierarchical clustering of samples. All biological replicates for healthy and periodontitis-affected had R2 (Spearman) correlation of gene expression (read counts) above 
0.92.Functional analyses of gene lists using WebGestaltFigure 3. Venn diagram of mRNA transcripts. Venn diagram showing genes that were uniquely expressed in periodontitis-affected (1375) and healthy (511) gingival tissues. The intersection of the two circles refers to transcripts, which are expressed in both periodontitisaffected and healthy gingival tissues (20 236). doi:10.1371/journal.pone.0046440.gAnalyses of gene categories and pathways was performed using the WEB-based Gene Set Analysis Toolkit v2 (WebGestalt) [23] with parameters: Id Type: Ensembl_gene_stable_id, Ref Set: Entrez Gene, Significance Level: p,0.05, Statistics Test: Hypergeometric, MTC: BH, Minimum: 2. KEGG analysis was used for pathway enrichment analysis and the Gene ontology (GO)Gene Expression in PeriodontitisTable 2. Enriched regulated (KEGG) biological pathways among unique genes in periodontitis-affected tissues.Pathway Neuroactive ligand-receptor interaction Cytokine-cytokine receptor interaction Chemokine signaling pathway Intestinal immune network for IgA production Alanine, aspartate and glutamate metabolism Tyrosine metabolism Calcium signaling pathway Hedgehog signaling pathway Systemic.
