ERX1371030 E-MTAB-4522:M_smegmatis_CO1 ERP014453 E-MTAB-4522 Monitoring global differential gene expression in context of protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis str. MC2 155 under hypochlorite stress. ERS1073928 SAMEA3886794 E-MTAB-4522:M_smegmatis_CO1 M_smegmatis_CO1 RNA-Seq TRANSCRIPTOMIC RANDOM For stress experiments Mycobacterium smegmatis mc2155 wild type strain was grown in modified Hartmans-de Bont minimal medium (HdB) (finally per liter: EDTA [0.01 g], MgCl2x6H2O [0.1 g], CaCl2x2H2O [1 mg], NaMoO4x2H2O [0.2 mg], CoCl2x6H2O [0.4 mg] , MnCl2x2H2O [1 mg] , ZnSO4x7H2O [2 mg] , FeSO4x7H2O [5 mg] , CuSO4x5H2O [0.2 mg]; complemented with 15 mM (NH4)2SO4, 0.05% Tween80, 27.4 mM glycerol, 50 mM MOPS; 8.90 mM K2HPO4 and 7.08 mM NaH2PO4; pH 7.0) at 37°C and vigorous agitation. 15% sodium hypochlorite (NaOCl) was purchased from Sigma Aldrich. After harvesting control samples cultures were exposed to 1 mM NaOCl at an optical density at 500 nm (OD500) of 0.4 – 0.45 in the early log phase. Briefly, M. smegmatis mc2155 cells of 3 replicate experiments were harvested before and 30 min after exposure to 1 mM NaOCl and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). 150 0 F Application Read Forward 1 1 R Application Read Reverse 76 Illumina HiSeq 1500 Experimental Factor: none stimulus ERX1371031 E-MTAB-4522:M_smegmatis_CO2 ERP014453 E-MTAB-4522 Monitoring global differential gene expression in context of protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis str. MC2 155 under hypochlorite stress. ERS1073929 SAMEA3886795 E-MTAB-4522:M_smegmatis_CO2 M_smegmatis_CO2 RNA-Seq TRANSCRIPTOMIC RANDOM For stress experiments Mycobacterium smegmatis mc2155 wild type strain was grown in modified Hartmans-de Bont minimal medium (HdB) (finally per liter: EDTA [0.01 g], MgCl2x6H2O [0.1 g], CaCl2x2H2O [1 mg], NaMoO4x2H2O [0.2 mg], CoCl2x6H2O [0.4 mg] , MnCl2x2H2O [1 mg] , ZnSO4x7H2O [2 mg] , FeSO4x7H2O [5 mg] , CuSO4x5H2O [0.2 mg]; complemented with 15 mM (NH4)2SO4, 0.05% Tween80, 27.4 mM glycerol, 50 mM MOPS; 8.90 mM K2HPO4 and 7.08 mM NaH2PO4; pH 7.0) at 37°C and vigorous agitation. 15% sodium hypochlorite (NaOCl) was purchased from Sigma Aldrich. After harvesting control samples cultures were exposed to 1 mM NaOCl at an optical density at 500 nm (OD500) of 0.4 – 0.45 in the early log phase. Briefly, M. smegmatis mc2155 cells of 3 replicate experiments were harvested before and 30 min after exposure to 1 mM NaOCl and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). 150 0 F Application Read Forward 1 1 R Application Read Reverse 76 Illumina MiSeq Experimental Factor: none stimulus ERX1371032 E-MTAB-4522:M_smegmatis_CO3 ERP014453 E-MTAB-4522 Monitoring global differential gene expression in context of protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis str. MC2 155 under hypochlorite stress. ERS1073930 SAMEA3886796 E-MTAB-4522:M_smegmatis_CO3 M_smegmatis_CO3 RNA-Seq TRANSCRIPTOMIC RANDOM For stress experiments Mycobacterium smegmatis mc2155 wild type strain was grown in modified Hartmans-de Bont minimal medium (HdB) (finally per liter: EDTA [0.01 g], MgCl2x6H2O [0.1 g], CaCl2x2H2O [1 mg], NaMoO4x2H2O [0.2 mg], CoCl2x6H2O [0.4 mg] , MnCl2x2H2O [1 mg] , ZnSO4x7H2O [2 mg] , FeSO4x7H2O [5 mg] , CuSO4x5H2O [0.2 mg]; complemented with 15 mM (NH4)2SO4, 0.05% Tween80, 27.4 mM glycerol, 50 mM MOPS; 8.90 mM K2HPO4 and 7.08 mM NaH2PO4; pH 7.0) at 37°C and vigorous agitation. 15% sodium hypochlorite (NaOCl) was purchased from Sigma Aldrich. After harvesting control samples cultures were exposed to 1 mM NaOCl at an optical density at 500 nm (OD500) of 0.4 – 0.45 in the early log phase. Briefly, M. smegmatis mc2155 cells of 3 replicate experiments were harvested before and 30 min after exposure to 1 mM NaOCl and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). 150 0 F Application Read Forward 1 1 R Application Read Reverse 76 Illumina HiSeq 1500 Experimental Factor: none stimulus ERX1371033 E-MTAB-4522:M_smegmatis_NaOCl1 ERP014453 E-MTAB-4522 Monitoring global differential gene expression in context of protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis str. MC2 155 under hypochlorite stress. ERS1073931 SAMEA3886797 E-MTAB-4522:M_smegmatis_NaOCl1 M_smegmatis_NaOCl1 RNA-Seq TRANSCRIPTOMIC RANDOM For stress experiments Mycobacterium smegmatis mc2155 wild type strain was grown in modified Hartmans-de Bont minimal medium (HdB) (finally per liter: EDTA [0.01 g], MgCl2x6H2O [0.1 g], CaCl2x2H2O [1 mg], NaMoO4x2H2O [0.2 mg], CoCl2x6H2O [0.4 mg] , MnCl2x2H2O [1 mg] , ZnSO4x7H2O [2 mg] , FeSO4x7H2O [5 mg] , CuSO4x5H2O [0.2 mg]; complemented with 15 mM (NH4)2SO4, 0.05% Tween80, 27.4 mM glycerol, 50 mM MOPS; 8.90 mM K2HPO4 and 7.08 mM NaH2PO4; pH 7.0) at 37°C and vigorous agitation. 15% sodium hypochlorite (NaOCl) was purchased from Sigma Aldrich. After harvesting control samples cultures were exposed to 1 mM NaOCl at an optical density at 500 nm (OD500) of 0.4 – 0.45 in the early log phase. Briefly, M. smegmatis mc2155 cells of 3 replicate experiments were harvested before and 30 min after exposure to 1 mM NaOCl and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). 150 0 F Application Read Forward 1 1 R Application Read Reverse 76 Illumina HiSeq 1500 Experimental Factor: 30 min 1mM NaOCl treatment in early log phase stimulus ERX1371034 E-MTAB-4522:M_smegmatis_NaOCl2 ERP014453 E-MTAB-4522 Monitoring global differential gene expression in context of protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis str. MC2 155 under hypochlorite stress. ERS1073932 SAMEA3886798 E-MTAB-4522:M_smegmatis_NaOCl2 M_smegmatis_NaOCl2 RNA-Seq TRANSCRIPTOMIC RANDOM For stress experiments Mycobacterium smegmatis mc2155 wild type strain was grown in modified Hartmans-de Bont minimal medium (HdB) (finally per liter: EDTA [0.01 g], MgCl2x6H2O [0.1 g], CaCl2x2H2O [1 mg], NaMoO4x2H2O [0.2 mg], CoCl2x6H2O [0.4 mg] , MnCl2x2H2O [1 mg] , ZnSO4x7H2O [2 mg] , FeSO4x7H2O [5 mg] , CuSO4x5H2O [0.2 mg]; complemented with 15 mM (NH4)2SO4, 0.05% Tween80, 27.4 mM glycerol, 50 mM MOPS; 8.90 mM K2HPO4 and 7.08 mM NaH2PO4; pH 7.0) at 37°C and vigorous agitation. 15% sodium hypochlorite (NaOCl) was purchased from Sigma Aldrich. After harvesting control samples cultures were exposed to 1 mM NaOCl at an optical density at 500 nm (OD500) of 0.4 – 0.45 in the early log phase. Briefly, M. smegmatis mc2155 cells of 3 replicate experiments were harvested before and 30 min after exposure to 1 mM NaOCl and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). 152 0 F Application Read Forward 1 1 R Application Read Reverse 77 Illumina MiSeq Experimental Factor: 30 min 1mM NaOCl treatment in early log phase stimulus ERX1371035 E-MTAB-4522:M_smegmatis_NaOCl3 ERP014453 E-MTAB-4522 Monitoring global differential gene expression in context of protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis str. MC2 155 under hypochlorite stress. ERS1073933 SAMEA3886799 E-MTAB-4522:M_smegmatis_NaOCl3 M_smegmatis_NaOCl3 RNA-Seq TRANSCRIPTOMIC RANDOM For stress experiments Mycobacterium smegmatis mc2155 wild type strain was grown in modified Hartmans-de Bont minimal medium (HdB) (finally per liter: EDTA [0.01 g], MgCl2x6H2O [0.1 g], CaCl2x2H2O [1 mg], NaMoO4x2H2O [0.2 mg], CoCl2x6H2O [0.4 mg] , MnCl2x2H2O [1 mg] , ZnSO4x7H2O [2 mg] , FeSO4x7H2O [5 mg] , CuSO4x5H2O [0.2 mg]; complemented with 15 mM (NH4)2SO4, 0.05% Tween80, 27.4 mM glycerol, 50 mM MOPS; 8.90 mM K2HPO4 and 7.08 mM NaH2PO4; pH 7.0) at 37°C and vigorous agitation. 15% sodium hypochlorite (NaOCl) was purchased from Sigma Aldrich. After harvesting control samples cultures were exposed to 1 mM NaOCl at an optical density at 500 nm (OD500) of 0.4 – 0.45 in the early log phase. Briefly, M. smegmatis mc2155 cells of 3 replicate experiments were harvested before and 30 min after exposure to 1 mM NaOCl and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). 150 0 F Application Read Forward 1 1 R Application Read Reverse 76 Illumina HiSeq 1500 Experimental Factor: 30 min 1mM NaOCl treatment in early log phase stimulus