ERX1224562 E-MTAB-4081:090mut_7830_ACAGTG_read1.fastq.gz E-MTAB-4081:090mut_7830_ACAGTG_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982793 SAMEA3675644 E-MTAB-4081:090mut_7830_ACAGTG_read1.fastq.gz 090mut_7830_ACAGTG_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN090 genotype ERX1224563 E-MTAB-4081:090mut_7830_ACAGTG_read2.fastq.gz E-MTAB-4081:090mut_7830_ACAGTG_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982794 SAMEA3675645 E-MTAB-4081:090mut_7830_ACAGTG_read2.fastq.gz 090mut_7830_ACAGTG_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN090 genotype ERX1224564 E-MTAB-4081:098mut_7831_GCCAAT_read1.fastq.gz E-MTAB-4081:098mut_7831_GCCAAT_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982795 SAMEA3675646 E-MTAB-4081:098mut_7831_GCCAAT_read1.fastq.gz 098mut_7831_GCCAAT_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN098 genotype ERX1224565 E-MTAB-4081:098mut_7831_GCCAAT_read2.fastq.gz E-MTAB-4081:098mut_7831_GCCAAT_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982796 SAMEA3675647 E-MTAB-4081:098mut_7831_GCCAAT_read2.fastq.gz 098mut_7831_GCCAAT_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN098 genotype ERX1224566 E-MTAB-4081:208mut_7828_TTAGGC_read1.fastq.gz E-MTAB-4081:208mut_7828_TTAGGC_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982797 SAMEA3675648 E-MTAB-4081:208mut_7828_TTAGGC_read1.fastq.gz 208mut_7828_TTAGGC_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN007 genotype ERX1224567 E-MTAB-4081:208mut_7828_TTAGGC_read2.fastq.gz E-MTAB-4081:208mut_7828_TTAGGC_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982798 SAMEA3675649 E-MTAB-4081:208mut_7828_TTAGGC_read2.fastq.gz 208mut_7828_TTAGGC_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN007 genotype ERX1224568 E-MTAB-4081:230mut_7826_ATCACG_read1.fastq.gz E-MTAB-4081:230mut_7826_ATCACG_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982799 SAMEA3675650 E-MTAB-4081:230mut_7826_ATCACG_read1.fastq.gz 230mut_7826_ATCACG_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN230 genotype ERX1224569 E-MTAB-4081:230mut_7826_ATCACG_read2.fastq.gz E-MTAB-4081:230mut_7826_ATCACG_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982800 SAMEA3675651 E-MTAB-4081:230mut_7826_ATCACG_read2.fastq.gz 230mut_7826_ATCACG_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN230 genotype ERX1224570 E-MTAB-4081:283mut_7833_ACTTGA_read1.fastq.gz E-MTAB-4081:283mut_7833_ACTTGA_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982801 SAMEA3675652 E-MTAB-4081:283mut_7833_ACTTGA_read1.fastq.gz 283mut_7833_ACTTGA_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN283 genotype ERX1224571 E-MTAB-4081:283mut_7833_ACTTGA_read2.fastq.gz E-MTAB-4081:283mut_7833_ACTTGA_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982802 SAMEA3675653 E-MTAB-4081:283mut_7833_ACTTGA_read2.fastq.gz 283mut_7833_ACTTGA_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN283 genotype ERX1224572 E-MTAB-4081:289mut_7827_CGATGT_read1.fastq.gz E-MTAB-4081:289mut_7827_CGATGT_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982803 SAMEA3675654 E-MTAB-4081:289mut_7827_CGATGT_read1.fastq.gz 289mut_7827_CGATGT_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN289 genotype ERX1224573 E-MTAB-4081:289mut_7827_CGATGT_read2.fastq.gz E-MTAB-4081:289mut_7827_CGATGT_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982804 SAMEA3675655 E-MTAB-4081:289mut_7827_CGATGT_read2.fastq.gz 289mut_7827_CGATGT_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN289 genotype ERX1224574 E-MTAB-4081:306mut_7836_GGCTAC_read1.fastq.gz E-MTAB-4081:306mut_7836_GGCTAC_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982805 SAMEA3675656 E-MTAB-4081:306mut_7836_GGCTAC_read1.fastq.gz 306mut_7836_GGCTAC_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN306 genotype ERX1224575 E-MTAB-4081:306mut_7836_GGCTAC_read2.fastq.gz E-MTAB-4081:306mut_7836_GGCTAC_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982806 SAMEA3675657 E-MTAB-4081:306mut_7836_GGCTAC_read2.fastq.gz 306mut_7836_GGCTAC_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN306 genotype ERX1224576 E-MTAB-4081:312mut_7837_CTTGTA_read1.fastq.gz E-MTAB-4081:312mut_7837_CTTGTA_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982807 SAMEA3675658 E-MTAB-4081:312mut_7837_CTTGTA_read1.fastq.gz 312mut_7837_CTTGTA_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN312 genotype ERX1224577 E-MTAB-4081:312mut_7837_CTTGTA_read2.fastq.gz E-MTAB-4081:312mut_7837_CTTGTA_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982808 SAMEA3675659 E-MTAB-4081:312mut_7837_CTTGTA_read2.fastq.gz 312mut_7837_CTTGTA_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN312 genotype ERX1224578 E-MTAB-4081:323mut_7838_AGTCAA_read1.fastq.gz E-MTAB-4081:323mut_7838_AGTCAA_read1.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982809 SAMEA3675660 E-MTAB-4081:323mut_7838_AGTCAA_read1.fastq.gz 323mut_7838_AGTCAA_read1.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN323 genotype ERX1224579 E-MTAB-4081:323mut_7838_AGTCAA_read2.fastq.gz E-MTAB-4081:323mut_7838_AGTCAA_read2.fastq.gz ERP013301 E-MTAB-4081 Bacterial antisense RNAs are mainly the product of transcriptional noise ERS982810 SAMEA3675661 E-MTAB-4081:323mut_7838_AGTCAA_read2.fastq.gz 323mut_7838_AGTCAA_read2.fastq.gz RNA-Seq TRANSCRIPTOMIC RT-PCR Mycoplasma pneumoniae cells were washed twice with PBS and lysated with 700 l of Qiazol buffer. RNA extractions were performed by using miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 g of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5 and 3 ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3 adapters and subsequently 5 adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3 RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries pas performed using 6% Novex TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 l of elution buffer. Illumina HiSeq 2000 Experimental Factor: Overexpression ncMPN323 genotype