SRX3456099 GSM2881195 SRP126361 SRS2744872 GSM2881195 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881195 GSM2881195 GEO Accession GSM2881195 SRX3456100 GSM2881196 SRP126361 SRS2744796 GSM2881196 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881196 GSM2881196 GEO Accession GSM2881196 SRX3456101 GSM2881197 SRP126361 SRS2744797 GSM2881197 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881197 GSM2881197 GEO Accession GSM2881197 SRX3456102 GSM2881198 SRP126361 SRS2744798 GSM2881198 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881198 GSM2881198 GEO Accession GSM2881198 SRX3456103 GSM2881199 SRP126361 SRS2744799 GSM2881199 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881199 GSM2881199 GEO Accession GSM2881199 SRX3456104 GSM2881200 SRP126361 SRS2744800 GSM2881200 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881200 GSM2881200 GEO Accession GSM2881200 SRX3456105 GSM2881201 SRP126361 SRS2744801 GSM2881201 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881201 GSM2881201 GEO Accession GSM2881201 SRX3456106 GSM2881202 SRP126361 SRS2744802 GSM2881202 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881202 GSM2881202 GEO Accession GSM2881202 SRX3456107 GSM2881203 SRP126361 SRS2744803 GSM2881203 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881203 GSM2881203 GEO Accession GSM2881203 SRX3456108 GSM2881204 SRP126361 SRS2744804 GSM2881204 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881204 GSM2881204 GEO Accession GSM2881204 SRX3456109 GSM2881205 SRP126361 SRS2744805 GSM2881205 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881205 GSM2881205 GEO Accession GSM2881205 SRX3456110 GSM2881206 SRP126361 SRS2744806 GSM2881206 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881206 GSM2881206 GEO Accession GSM2881206 SRX3456111 GSM2881207 SRP126361 SRS2744809 GSM2881207 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881207 GSM2881207 GEO Accession GSM2881207 SRX3456112 GSM2881208 SRP126361 SRS2744807 GSM2881208 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881208 GSM2881208 GEO Accession GSM2881208 SRX3456113 GSM2881209 SRP126361 SRS2744808 GSM2881209 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881209 GSM2881209 GEO Accession GSM2881209 SRX3456114 GSM2881210 SRP126361 SRS2744811 GSM2881210 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881210 GSM2881210 GEO Accession GSM2881210 SRX3456115 GSM2881211 SRP126361 SRS2744810 GSM2881211 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881211 GSM2881211 GEO Accession GSM2881211 SRX3456116 GSM2881212 SRP126361 SRS2744812 GSM2881212 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881212 GSM2881212 GEO Accession GSM2881212 SRX3456117 GSM2881213 SRP126361 SRS2744813 GSM2881213 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881213 GSM2881213 GEO Accession GSM2881213 SRX3456118 GSM2881214 SRP126361 SRS2744814 GSM2881214 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881214 GSM2881214 GEO Accession GSM2881214 SRX3456119 GSM2881215 SRP126361 SRS2744815 GSM2881215 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881215 GSM2881215 GEO Accession GSM2881215 SRX3456120 GSM2881216 SRP126361 SRS2744816 GSM2881216 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881216 GSM2881216 GEO Accession GSM2881216 SRX3456121 GSM2881217 SRP126361 SRS2744817 GSM2881217 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881217 GSM2881217 GEO Accession GSM2881217 SRX3456122 GSM2881218 SRP126361 SRS2744818 GSM2881218 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881218 GSM2881218 GEO Accession GSM2881218 SRX3456123 GSM2881219 SRP126361 SRS2744819 GSM2881219 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881219 GSM2881219 GEO Accession GSM2881219 SRX3456124 GSM2881220 SRP126361 SRS2744820 GSM2881220 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881220 GSM2881220 GEO Accession GSM2881220 SRX3456125 GSM2881221 SRP126361 SRS2744821 GSM2881221 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881221 GSM2881221 GEO Accession GSM2881221 SRX3456126 GSM2881222 SRP126361 SRS2744822 GSM2881222 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881222 GSM2881222 GEO Accession GSM2881222 SRX3456127 GSM2881223 SRP126361 SRS2744823 GSM2881223 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881223 GSM2881223 GEO Accession GSM2881223 SRX3456128 GSM2881224 SRP126361 SRS2744824 GSM2881224 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881224 GSM2881224 GEO Accession GSM2881224 SRX3456129 GSM2881225 SRP126361 SRS2744825 GSM2881225 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881225 GSM2881225 GEO Accession GSM2881225 SRX3456130 GSM2881226 SRP126361 SRS2744826 GSM2881226 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881226 GSM2881226 GEO Accession GSM2881226 SRX3456131 GSM2881227 SRP126361 SRS2744828 GSM2881227 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881227 GSM2881227 GEO Accession GSM2881227 SRX3456132 GSM2881228 SRP126361 SRS2744827 GSM2881228 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881228 GSM2881228 GEO Accession GSM2881228 SRX3456133 GSM2881229 SRP126361 SRS2744829 GSM2881229 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881229 GSM2881229 GEO Accession GSM2881229 SRX3456134 GSM2881230 SRP126361 SRS2744831 GSM2881230 RNA-Seq TRANSCRIPTOMIC cDNA RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol. The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer's instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82. Illumina HiSeq 2000 gds 302881230 GSM2881230 GEO Accession GSM2881230