SRX373342 GSM1259843 SRP032547 GSE52111 SRS498746 GSM1259843 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using RNeasy mini kit (Qiagen) with some alterations in the bacterial cell lyses procedure. Lyses was performed as described in França et al., PLoS One 2012. In brief, biofilm pellets were suspended in 500 µL of in the lyses buffer provided by the kit plus 500 µL of phenol. This supension was then transfered into Lysing Matrix B tubes (MPBiomedicals) and using a FastPrep BioSavan101 (Therno Scientific) the cells were lysed. Finally, the tubes were centrifuged and the suspension transfered into a new tube. An equal volume of 70% of ethanol was added. The suspension was transfered to the RNeasy mini kit columns and following the manufacturer's instructions total RNA was isolated. Thereafter, total RNA was treated with TURBO DNase (Ambion) and 1:5 Acid-phenol:chloroform in order to remove genomic DNA. Additionally total RNA was treated with MICROBEnrichTM (Ambion) and Ribo-ZeroTM rRNA removal kit for Gram-positive bacteria (Epicentre) to remove eukaryotic RNA and bacterial ribosomal RNA, respectively. Libraries were prepared according to Illumina's TruSeq RNA Sample Prep kit version 2. Briefly, 400 ng of previosuly purified mRNA was fragmented and used for the synthesis of double stranded complementary DNA. Thereafter, end-repair, single ‘A’ nucleotide addition to the 3' end of the blunt fragments, adaptor ligation and DNA fragments enrichment was performed to complete libraries construction. Validation of the constructed libraries was assessed through quantitative PCR and Agilent 2200 TapeStation High SensitivityD1K ScreenTapes. Illumina MiSeq GEO Sample GSM1259843 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1259843 gds 301259843 GEO Accession GSM1259843 SRX373343 GSM1259844 SRP032547 GSE52111 SRS498747 GSM1259844 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using RNeasy mini kit (Qiagen) with some alterations in the bacterial cell lyses procedure. Lyses was performed as described in França et al., PLoS One 2012. In brief, biofilm pellets were suspended in 500 µL of in the lyses buffer provided by the kit plus 500 µL of phenol. This supension was then transfered into Lysing Matrix B tubes (MPBiomedicals) and using a FastPrep BioSavan101 (Therno Scientific) the cells were lysed. Finally, the tubes were centrifuged and the suspension transfered into a new tube. An equal volume of 70% of ethanol was added. The suspension was transfered to the RNeasy mini kit columns and following the manufacturer's instructions total RNA was isolated. Thereafter, total RNA was treated with TURBO DNase (Ambion) and 1:5 Acid-phenol:chloroform in order to remove genomic DNA. Additionally total RNA was treated with MICROBEnrichTM (Ambion) and Ribo-ZeroTM rRNA removal kit for Gram-positive bacteria (Epicentre) to remove eukaryotic RNA and bacterial ribosomal RNA, respectively. Libraries were prepared according to Illumina's TruSeq RNA Sample Prep kit version 2. Briefly, 400 ng of previosuly purified mRNA was fragmented and used for the synthesis of double stranded complementary DNA. Thereafter, end-repair, single ‘A’ nucleotide addition to the 3' end of the blunt fragments, adaptor ligation and DNA fragments enrichment was performed to complete libraries construction. Validation of the constructed libraries was assessed through quantitative PCR and Agilent 2200 TapeStation High SensitivityD1K ScreenTapes. Illumina MiSeq GEO Sample GSM1259844 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1259844 gds 301259844 GEO Accession GSM1259844 SRX373344 GSM1259845 SRP032547 GSE52111 SRS498748 GSM1259845 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using RNeasy mini kit (Qiagen) with some alterations in the bacterial cell lyses procedure. Lyses was performed as described in França et al., PLoS One 2012. In brief, biofilm pellets were suspended in 500 µL of in the lyses buffer provided by the kit plus 500 µL of phenol. This supension was then transfered into Lysing Matrix B tubes (MPBiomedicals) and using a FastPrep BioSavan101 (Therno Scientific) the cells were lysed. Finally, the tubes were centrifuged and the suspension transfered into a new tube. An equal volume of 70% of ethanol was added. The suspension was transfered to the RNeasy mini kit columns and following the manufacturer's instructions total RNA was isolated. Thereafter, total RNA was treated with TURBO DNase (Ambion) and 1:5 Acid-phenol:chloroform in order to remove genomic DNA. Additionally total RNA was treated with MICROBEnrichTM (Ambion) and Ribo-ZeroTM rRNA removal kit for Gram-positive bacteria (Epicentre) to remove eukaryotic RNA and bacterial ribosomal RNA, respectively. Libraries were prepared according to Illumina's TruSeq RNA Sample Prep kit version 2. Briefly, 400 ng of previosuly purified mRNA was fragmented and used for the synthesis of double stranded complementary DNA. Thereafter, end-repair, single ‘A’ nucleotide addition to the 3' end of the blunt fragments, adaptor ligation and DNA fragments enrichment was performed to complete libraries construction. Validation of the constructed libraries was assessed through quantitative PCR and Agilent 2200 TapeStation High SensitivityD1K ScreenTapes. Illumina MiSeq GEO Sample GSM1259845 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1259845 gds 301259845 GEO Accession GSM1259845 SRX373345 GSM1259846 SRP032547 GSE52111 SRS498749 GSM1259846 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using RNeasy mini kit (Qiagen) with some alterations in the bacterial cell lyses procedure. Lyses was performed as described in França et al., PLoS One 2012. In brief, biofilm pellets were suspended in 500 µL of in the lyses buffer provided by the kit plus 500 µL of phenol. This supension was then transfered into Lysing Matrix B tubes (MPBiomedicals) and using a FastPrep BioSavan101 (Therno Scientific) the cells were lysed. Finally, the tubes were centrifuged and the suspension transfered into a new tube. An equal volume of 70% of ethanol was added. The suspension was transfered to the RNeasy mini kit columns and following the manufacturer's instructions total RNA was isolated. Thereafter, total RNA was treated with TURBO DNase (Ambion) and 1:5 Acid-phenol:chloroform in order to remove genomic DNA. Additionally total RNA was treated with MICROBEnrichTM (Ambion) and Ribo-ZeroTM rRNA removal kit for Gram-positive bacteria (Epicentre) to remove eukaryotic RNA and bacterial ribosomal RNA, respectively. Libraries were prepared according to Illumina's TruSeq RNA Sample Prep kit version 2. Briefly, 400 ng of previosuly purified mRNA was fragmented and used for the synthesis of double stranded complementary DNA. Thereafter, end-repair, single ‘A’ nucleotide addition to the 3' end of the blunt fragments, adaptor ligation and DNA fragments enrichment was performed to complete libraries construction. Validation of the constructed libraries was assessed through quantitative PCR and Agilent 2200 TapeStation High SensitivityD1K ScreenTapes. Illumina MiSeq GEO Sample GSM1259846 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1259846 gds 301259846 GEO Accession GSM1259846 SRX373346 GSM1259847 SRP032547 GSE52111 SRS498750 GSM1259847 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was extracted using RNeasy mini kit (Qiagen) with some alterations in the bacterial cell lyses procedure. Lyses was performed as described in França et al., PLoS One 2012. In brief, biofilm pellets were suspended in 500 µL of in the lyses buffer provided by the kit plus 500 µL of phenol. This supension was then transfered into Lysing Matrix B tubes (MPBiomedicals) and using a FastPrep BioSavan101 (Therno Scientific) the cells were lysed. Finally, the tubes were centrifuged and the suspension transfered into a new tube. An equal volume of 70% of ethanol was added. The suspension was transfered to the RNeasy mini kit columns and following the manufacturer's instructions total RNA was isolated. Thereafter, total RNA was treated with TURBO DNase (Ambion) and 1:5 Acid-phenol:chloroform in order to remove genomic DNA. Additionally total RNA was treated with MICROBEnrichTM (Ambion) and Ribo-ZeroTM rRNA removal kit for Gram-positive bacteria (Epicentre) to remove eukaryotic RNA and bacterial ribosomal RNA, respectively. Libraries were prepared according to Illumina's TruSeq RNA Sample Prep kit version 2. Briefly, 400 ng of previosuly purified mRNA was fragmented and used for the synthesis of double stranded complementary DNA. Thereafter, end-repair, single ‘A’ nucleotide addition to the 3' end of the blunt fragments, adaptor ligation and DNA fragments enrichment was performed to complete libraries construction. Validation of the constructed libraries was assessed through quantitative PCR and Agilent 2200 TapeStation High SensitivityD1K ScreenTapes. Illumina MiSeq GEO Sample GSM1259847 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1259847 gds 301259847 GEO Accession GSM1259847