REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Flag Monoclonal Antibody	Sigma	Cat#F3165; RRID: AB_262044
Bacterial and Virus Strains
Mycoplasma pneumoniae M129	Colleague	Richard Herrmann
Mycoplasma pneumoniae strains	this paper	Mendeley: [doi:10.17632/xf6y59gz6c.1]
Chemicals, Peptides, and Recombinant Proteins
6-Thioguanine	Sigma	Cat#A4882
Azithromycin	Sigma	Cat#75199
CCCP	Sigma	Cat#C2759
Ciprofloxacin	Sigma	Cat#17850
Clarythromycin	Sigma	Cat#C9742
Cytochalasin B	Sigma	Cat#C8273
DCCD	Sigma	Cat#D80002
Diamide	Sigma	Cat#D3648
Doxycycline	Sigma	Cat#D9891
Erythromycin	Sigma	Cat#E5389
Gemcitabine	Sigma	Cat#G6423
Levofloxacin	Sigma	Cat#28266
Minocycline	Sigma	Cat#M9511
Mitomycin C	Sigma	Cat#M4287
Norfloxacin	Sigma	Cat#N9890
Plasmocin	Invivogen	Cat#ant-mpp
Pyocyanin	Sigma	Cat#P0046
Sanguinarine	Sigma	Cat#S5890
Spectinomycin	Sigma	Cat#S4014
Spiramycin	Sigma	Cat#S9132
Streptomycin	Sigma	Cat#S6501
T-butyl hydroperoxide	Sigma	Cat#458139
Tetracycline	Sigma	Cat#T3258
Thiolutin	Fermentek	Cat#87-11-6
Valinomycin	Sigma	Cat#V0627
Critical Commercial Assays
NebNExt Ultra kit	New England Biolabs	Cat#E7370L
RNA Isolation Kit: RNeasy Mini Kit	Qiagen	Cat#74004
RNA Isolation Kit: miRNeasy mini kit
TruSeq smallSmall RNA Sample Prep Kit	Illumina	Cat#RS-200-0012
Phosphopeptide Enrichment kit	Thermo Scientific	Cat#88301
Deposited Data
RNA-Seq: Phenome analysis of Mycoplasma pneumoniae	this paper	ArrayExpress E-MTAB-3771
RNA-seq: Transcriptome analysis of Mycoplasma pneumoniae I	this paper	ArrayExpress E-MTAB-3772
RNA-seq: Transcriptome analysis of Mycoplasma pneumoniae II
RNA-seq: Transcriptome analysis of Mycoplasma pneumoniae III	this paper	ArrayExpress E-MTAB-4642
DNase proteccion: Protein occupancy of Mycoplasma pneumoniae chromosome	this paper	ArrayExpress E-MTAB-3783
RNA-seq: Transcriptome analysis of Mycoplasma pneumoniae IV	this paper	ArrayExpress E-MTAB-4784
ChIP-seq of Mycoplasma pneumoniae putative Transcription factors	this paper	ArrayExpress E-MTAB-5944
RNA-seq: 5'′-end mapping of totalTotal Mycoplasma pneumoniae RNA	this paper	ArrayExpress E-MTAB-6124
RNA-seq: Transcriptome analysis of Mycoplasma pneumoniae V	this paper	ArrayExpress E-MTAB-6229
RNA-seq: Transcriptome analysis of Mycoplasma pneumoniae VI	this paper	ArrayExpress E-MTAB-7153
Proteomics: Mycoplasma pneumoniae Chromatin isolation	this paper	ProteomeXchange XD007672
Proteomics: DNA Affinity chromatography on Mycoplasma pneumoniae extracts I (RNA elution)	this paper	ProteomeXchange PXD007674
Proteomics: DNA Affinity chromatography on Mycoplasma pneumoniae extracts II (cellulose column)	this paper	ProteomeXchange PXD007676
Proteomics: DNA Affinity chromatography on Mycoplasma pneumoniae extracts III (DNA column)	this paper	ProteomeXchange PXD007677
Proteomics: TF overexpression and mutant data	this paper	ProteomeXchange PXD007551, PXD007537, PXD007545, PXD007557, PXD007558, PXD007560, PXD007561, PXD007565, PXD007566, PXD007658, PXD007658.
Oligonucleotides
Oligonucleotides	this paper	Mendeley: [doi:10.17632/xf6y59gz6c.1]
Recombinant DNA
Plasmids	this paper	Mendeley: [doi:10.17632/xf6y59gz6c.1]
Software and Algorithms
Xcalibur software v3.0.63	Thermo Fisher Scientific	https://www.thermofisher.com/order/catalog/product/OPTON-30487
Proteome Discoverer software suite v2.0	Thermo Fisher Scientific	https://www.thermofisher.com/order/catalog/product/OPTON-30795
MAQ software	Li et al., 2008	N/A
Inferelator software	Bonneau et al., 2006	https://github.com/simonsfoundation/inferelator_ng
R version 3.5.1	R Core Team, 2018
tidyverse (R packages ; version 1.2.1)	Wickham et al., 2017	R package
ggpubr (R package ; version 0.2)	Kassambara, 2018	R package
Gdata (R package ; version 2.18.0)	Warnes et al., 2017	R package
DESeq2 (R package ; version 1.22.2)	Love et al., 2014	R package
NbClust (R package ; version 3.0)	Charrad et al., 2014	R package
randomForest (R package ; version 4.6-14)	Liaw and Wiener, 2002	R package
Cytoscape (Version 3.6.0)	Shannon et al., 2003	https://cytoscape.org/
clusterMaker2 (Cytoscape plugin, version 1.2.1)	Morris et al., 2011	Cytoscape plugin