GENES 2885:::Strain.1843...replicate.2 2885:::Strain.3160..replicate.1 2885:::Strain.3160..replicate.2 2885:::Strain.9802501..replicate.4 2885:::Strain.9802501..replicate1 4062:::H37Rv.ctrl.vs.Rv3132.34.KO..complemented...0.05.mM.DETA.NO.40min.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.005.mM.DETA.NO.40min.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.005.mM.DETA.NO.40min.rep.4 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.05.mM.DETA.NO.rep.3 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.01.mM.DETA.NO.rep.2 4068:::H37Rv.delta.mprAB.mutant.vs..H37Rv.delta.mprAB.mutant.SDS.treated.rep.4 4084:::High.iron.wt.vs.low.iron.wt.3b 4089:::H37Rv.whiB7.null.ethanol.vs..1.0.ug.ml.Tetracyclin.for.15.min.rep.2 4089:::H37Rv.whiB7.null.ethanol.vs..1.0.ug.ml.Tetracyclin.for.2.hr.rep.2 4089:::H37Rv.whiB7.null.vs..H37Rv.whiB7.null.with.whiB7.over.expression.rep.3 4089:::MTB1254.control.vs..1.0.ug.ml.Erythromycin.for.2.hr..ref..rep.3 4089:::MTB1254.control.vs..1.0.ug.ml.Erythromycin.for.2.hr..ref..rep.4 4089:::MTB1254.control.vs..1.0.ug.ml.Erythromycin.for.24.hr..ref..rep.1 4089:::MTB1254.control.vs..1.0.ug.ml.Erythromycin.for.24.hr..ref..rep.5 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Erythromycin.for.15.min.rep.2 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Tetracyclin.for.15.min.rep.2 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Tetracyclin.for.30.min.rep.3 4089:::MTB1254.ethanol.vs..1.0.ug.ml.Erythromycin.for.30.min.rep.3 4089:::MTB1254.ethanol.vs..1.0.ug.ml.Erythromycin.for.30.min.rep.4 4089:::MTB1254.ethanol.vs..1.0.ug.ml.Tetracyclin.for.15.min.rep.4 4089:::MTB1254.ethanol.vs..1.0.ug.ml.Tetracyclin.for.2.hr.rep.4 4089:::MTB1254.ethanol.vs..1.0.ug.ml.Tetracyclin.for.30.min.rep.1 4089:::MTB1254.ethanol.vs..100.ug.ml.Erythromycin.for.15.min.rep.1 4089:::MTB1254.ethanol.vs..100.ug.ml.Erythromycin.for.15.min.rep.2 4089:::MTB1254.ethanol.vs..100.ug.ml.Tetracyclin.for.15.min.rep.1 4089:::MTB1254.ethanol.vs..100.ug.ml.Tetracyclin.for.30.min.rep.3 4089:::MTB1254.ethanol.vs..100.ug.ml.Tetracyclin.for.30.min.rep.4 4089:::MTB1254.ethanol.vs..25.ug.ml.Erythromycin.for.15.min.rep.1 4089:::MTB1254.ethanol.vs..25.ug.ml.Erythromycin.for.15.min.rep.4 4089:::MTB1254.ethanol.vs..25.ug.ml.Tetracyclin.for.30.min.rep.4 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Erythromycin.for.15.min.rep.2 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Erythromycin.for.30.min.rep.4 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Tetracyclin.for.15.min.rep.4 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Tetracyclin.for.30.min.rep.1 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Tetracyclin.for.30.min.rep.4 4089:::MTB1254.vs..MTB1254.rep2 4089:::MTB1254.vs..MTB1254.rep6 4101:::H37Rv.Day.0.rep.1 4101:::H37Rv.Day.0.vs.low.Oxygen.Day.4.rep.1 4101:::H37Rv.Day14.2 4101:::H37Rv.Day24.3 4101:::NRP.Day10..1 4101:::NRP.Day14..2 4101:::NRP.Day8..1 4107:::DIPED..100ug.mL..DMSO..12h..2 4107:::DIPED..100ug.mL..DMSO..12h..3 4107:::DIPED..50ug.mL..DMSO..12h 4107:::EMB.10ug.mL.vs.DMSO.12h.3 4107:::H2O2.4mM.vs.ctrl.12h.1 4107:::H2O2.4mM.vs.ctrl.8h.1 4107:::Mtm.0.2ug.mL.vs.ctrl.12h.1 4107:::Mtm.0.2ug.mL.vs.ctrl.8h.2 4107:::PBS.Tween.7H9 4107:::pH4.8vspH6.8..2h. 4107:::pH5.6vspH6.8..2h.A 4107:::UV.40J.vs.8h.2 4107:::UV.40J.vs.ctrl.12h.1 4107:::UV.40J.vs.ctrl.8h.1 4107:::X.109..10ug.mL..DMSO..12h..replicate.2..GEO.acc..GSM28054. 4107:::X.241..0.1ug.mL..DMSO..12h..1..GEO.acc.GSM28046. 4107:::X0.12mg.mL.BZAvspH5.6..7h. 4107:::X0.12mg.mL.NamvspH5.6..7h. 4107:::X0.12mg.mL.PZAvspH5.6..11h. 4107:::X0.12mg.mL.PZAvspH5.6..5.5h. 4107:::X0.12mg.mL.PZAvspH5.6..6h. 4107:::X0.12mg.mL.PZAvspH5.6..6h.A 4107:::X0.1mg.mL.TriclosanvsEtOH..6h 4107:::X0.1ug.mL.Mtmvsctrl..0.33h. 4107:::X0.1ug.mL.Mtmvsctrl..1.5h. 4107:::X0.2mg.mL.AmpvsEtOH..6hB 4107:::X0.2ug.mL.Mtm.ctrl..4h...2 4107:::X1.2mg.mL.NamvspH5.6..5h. 4107:::X1.2mg.mL.PZA.pH5.6..5h. 4107:::X1.2mg.mL.PZAvspH5.6..4h.A 4107:::X1.2mg.mL.PZAvspH5.6..6h.A 4107:::X1.2mg.mL.PZAvspH5.6..7h.A 4107:::X100ug.mLCephalexinvsEtOH.6hA 4107:::X10ug.mL..109vsDMSO..6h 4107:::X10ug.mL..241.DMSO..6h 4107:::X10ug.mL..241vsDMSO..6h 4107:::X10ug.mL..59.DMSO..6h 4107:::X10ug.mL..59vsDMSO..6hA 4107:::X10ug.mL.capreomycinvsEtOH..6h 4107:::X10ug.mL.clotrimvsEtOH..6h 4107:::X10ug.mL.RoxvsEtOH..6h 4107:::X10ug.mL.RoxvsEtOH..6hA 4107:::X10ug.mL.TetvsEtOH..6h 4107:::X10ug.mL.TetvsEtOH..6hA 4107:::X10ug.mL.TriclosanvsDMSO..6h 4107:::X10ug.mL.TriclosanvsDMSO..6hA 4107:::X10ug.mL.TRZ.DMSO..6h..1 4107:::X10ug.mL.TRZ.DMSO..6h..2 4107:::X13ug.mL.clfzine.DMSO..6h..1 4107:::X13ug.mL.clfzine.DMSO..6h..2 4107:::X200uM.Dipyridylvsctrl..6hA 4107:::X20mJ.UVvsctrl..6h. 4107:::X20ug.mL.Cephalexin.Ctrl..6h..1 4107:::X20ug.mL.chlorprmz.DMSO..6h..2 4107:::X20ug.mL.Procept.6776vsDMSO..6h 4107:::X24ug.mL.Econazole.DMSO..6h..2 4107:::X25J.UV.ctrl..2h. 4107:::X2ug.mL..111895vsDMSO..6h 4107:::X2ug.mL..111895vsDMSO..6hA 4107:::X2ug.mL..121940vsDMSO..6hA 4107:::X30ug.mL.RoxvsEtOH..6h 4107:::X30ug.mL.RoxvsEtOH..6hA 4107:::X40ug.mL.5CL.pH5.6..2h..2 4107:::X40ug.mL.5CL.pH5.6..4h..2 4107:::X4mM.H2O2.ctrl..2h...2 4107:::X4mM.H2O2vsctrl..2h. 4107:::X4mM.H2O2vsctrl..4h. 4107:::X4ug.mLNaturalcompoundvsDMSO.6h 4107:::X50ug.mL.RoxvsEtOH..6hA 4107:::X5ug.mL.CFZ.0.1mM.GSNO.DMSO..1 4107:::X5ug.mL.CFZ.0.1mM.GSNO.DMSO..2 4107:::X5ug.mLCFZ.0.1mMGSNOvsDMSO.A 4107:::X5ug.mLProcept.6778vsDMSO.6hA 4107:::X9ug.mLAscidideminNpvsDMSO.6h 4363:::H37Rv.hypoxia.1.day.rep.7 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC..OD.0.3.1 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC..OD.1.0.5 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD1.5.1 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD1.5.3 4523:::H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.5 4523:::H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.6 4523:::H37Rv.wild.type.vs.H37Rv.sigB.null.mutant.rep.4 4523:::H37Rv.wild.type.Vs.H37Rv.wild.type.rep.5 4575:::Whole.Lung.Surfactant.2hrs.rep.1 4581:::H37Rv.Ctrl.vs.10.ug.ml.garlic.extract.6hrs 4581:::H37Rv.Ctrl.vs.5.ug.ml.garlic.extract.6hrs 4615:::AA_10uM_10.min_01 4615:::AA_30uM_10.min_05 4615:::AA_30uM_1h_03 4615:::AA_30uM_1h_05 4615:::AA_30uM_2h_01 4615:::AA_30uM_2h_04 4615:::AA_30uM_2h_09 4615:::AA_30uM_30min_04 4615:::AA_30uM_30min_06 4615:::AA_30uM_4h_04 4615:::AA_30uM_4h_08 4615:::AA_60uM_2h_T0_03 4615:::aceatate.induction.2 4615:::Acetate.3mM.10m_04 4615:::Acetate.3mM.10m.07 4615:::Acetate.3mM.2h.03 4615:::Acetate.3mM.30m.01 4615:::Acetate.3mM.30m.07 4615:::C2_ceramide_25uM_1h_01 4615:::CHP.AA.24h.1 4615:::ETYA_30uM_10min.02 4615:::Glucose_20mM_1h.OA_50uM_10min 4615:::L2A_30uM_1h_03 4615:::L2A_30uM_2h_05 4615:::L2A_30uM_30Min_06 4615:::L2A_30uM_4h_06 4615:::MDGCy3.7H9Cy5.02 4615:::MTB1254_Bottom_14D_04 4615:::MTB1254_FA5_10min_04 4615:::MTB1254_Pellicle_14D_03 4615:::MTB1254_Pellicle_14D_04 4615:::MTB1254_Pellicle_21D_01 4615:::MTB1254_Pellicle_21D_02 4615:::MTB1254_Pellicle_21D_03 4615:::MTB1254_Pellicle_21D_04 4615:::MTB1254_Pellicle_42D_01 4615:::MTB1254.0485.1._OA_10m_03 4615:::MTB1254.3219.1._01 4615:::MTB1254.B4.1._PA_10MIN_01 4615:::MTB1254.B4.1._PA_30MIN_02 4615:::MTB1254.B4.1._PA_30MIN_03 4615:::MTB1254.B4.1.Compl._OA_30MIN_04 4615:::OA_50uM_10min_02 4615:::OA_50uM_10min_06 4615:::OA_50uM_1h_05 4615:::OA_50uM_2h_07 4615:::OA_50uM_2h..1.0..BSA.10mMGlu._30.min._01 4615:::OA_50uM_2h.1.5..BSA_30min_01 4615:::OA_50uM_30min_06 4615:::OA_50uM_4h_03 4615:::PA_50uM_10min_10 4615:::PA_50uM_1h_02 4615:::PA_50uM_24h.PA_100uM_1h_01 4615:::PA_50uM_2h_T0_02 4615:::PA_50uM_30min_09 4615:::PA_50uM.OA_10uM_4h_01 4615:::PA_50uM.OA_30uM_24h_01 4615:::Rv.MT90_100603_01 4615:::Starvation_1254_12h_02 4615:::Starvation_1254_12h_03 4615:::Starvation_1254_24h_02 4615:::Starvation_1254_24h_04 4615:::Starvation_1254_24h_05 4615:::Starvation_1254_6h_01 4615:::Starvation_1254_6h_04 4615:::Starvation_1254_OA50_6h_02 4615:::Starvation_1254_OA50_6h_04 4615:::Starvation_1254_PA50_24h_01 4615:::Starvation_1254_PA50.OA30_6h_04 4615:::Strain95.OA.10M.01 4615:::TBD097 4615:::TBD425 4615:::TBE055 4615:::TBE283 4615:::Test.6 4615:::Test.G.OA 4615:::Tet_100uM_30M_01 4615:::Tet_20uM_30M_01 4696:::H37Rv.wt.vs.dosS.dosT.null.anaerobic.Gaspak.4hr.rep.2 4696:::H37Rv.wt.vs.dosT.null.anaerobic.Gaspak24hr.rep.3 4696:::H37Rv.wt.vs.dosT.null.nitric.oxide.treatment.1hr.rep.2 4696:::H37Rv.wt.vs.dosT.null.nitric.oxide.treatment.1hr.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.1500.03_Beijing.rep.3 4699:::CDC1551.Ctrl.vs.clinical.isolate.4130.02_Haarlem.rep.2 4699:::CDC1551.Ctrl.vs.H37Rv.rep.3 4703:::Clinical.isolate.12954.03_Beijing.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.2333.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.resting.macrophages.rep.2 4704:::Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.2 4729:::H37Rv.wild.type.vs.PepD.null.mutant.rep.1 4731:::X10ug.ml.capreomycin.vs.Ethanol..6hrs 4731:::X10ug.ml.Ethambutol.vs.DMSO.12hrs.3 4731:::X12ug.ml.Ethionamide.vs.Ethanol.6hrs.rep.1 4735:::BCG.wild.type.vs.BCG.with.empty.pMV361.at.OD.0.2.rep.3 4735:::BCG.wild.type.vs.BCG.with.pMFdosR.at.OD.0.2.rep.4 4795:::CDC1551.ctrl.vs.10.ug.ml.Thioridazine.2hr.rep.1 4799:::H37Rv.ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.1 4799:::H37Rv.ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.2 4799:::H37Rv.ctrl.vs.1ug.ml.Isoniazid.for.6hrs.rep.1 4799:::H37Rv.KatG.null..ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.3 4799:::H37Rv.mouse.hallow.fiber..ctrl.vs.25mg.kg.Isoniazid.3rd.dose.6hrs.rep.1 4799:::H37Rv.O2.depleted..ctrl.vs.1ug.ml.Isoniazid.for.2hrs.rep.3 4802:::H37Rv.ctrl.vs.relE2.overexpression.24.hr.rep.2 4802:::H37Rv.ctrl.vs.relE3.overexpression.24.hr.rep.1 4860:::M..bovis.nadABC.null.nicotinamide.starvation.rep.2 Rohde_CellHostMicrobe2007:::CDC1551.in.ctrl.vs.100.nM.Concanamycin.A.treated.macrophages.for.2.hr Rohde_CellHostMicrobe2007:::M..bovis.ctrl..vs.24.hr.after.macrophage.infection Schnappinger_JEM2003:::MTB.in.Wild.type.macrophages...IFNg.for.24hrs RV0010C -0.47707882987369 -1.03641263041526 -0.47707882987369 0.246764912003632 0.50998081814084 0.208298616897184 1.15060188381302 1.14068290205601 0.119027781084105 -0.178541671626157 NA -0.642372151882472 -0.364589599717078 -0.109376879915124 -1.75003007864198 -0.947932959264404 -1.8594069585571 -0.328130639745371 -0.656261279490741 0.692720239462449 0.51042543960391 1.13022775912294 0.583343359547326 1.34898151895319 0.437507519660494 0.328130639745371 1.96878383847222 -0.401048559688786 0.656261279490741 -1.3854404789249 0.51042543960391 -1.78648903861368 0.328130639745371 -0.0729179199434157 -1.78648903861368 -0.51042543960391 1.09376879915124 0 2.15107863833076 1.20314567906636 -0.218753759830247 0 0.674490759476595 0.780989300446584 -2.30746838768309 NA 0.85198832775991 -0.603491732163269 0.496993191193281 0.652732993041866 0.456913095129307 0.935583956693342 1.37073928538792 0.565701927302951 1.04437278886699 0.0435155328694578 0.630975226607138 NA NA 1.00085725599753 0.19581989791256 1.02261502243226 0.58745969373768 1.06613055530172 1.54480141686575 0.674490759476595 1.08788832173644 0.78327959165024 0.935583956693342 -0.0217577664347289 0.739764058780782 1.08788832173644 0.892068423823884 0.58745969373768 0.0652732993041866 1.52304365043102 0.152304365043102 0.0217577664347289 3.04608730086204 1.21843492034482 NA 0.565701927302951 -0.304608730086204 -3.30718049807879 -0.9790994895628 -2.34983877495072 -0.304608730086204 -0.739764058780782 -0.652732993041866 -0.609217460172409 -0.892068423823884 -2.02347227842979 -1.8058946140825 -3.02432953442731 -2.34983877495072 -1.74062131477831 -2.00171451199506 -1.84941014695195 -1.54480141686575 -0.174062131477831 0.870310657389155 -0.239335430782018 -1.283708219649 -0.0652732993041866 -2.1105033441687 0.739764058780782 -0.0435155328694577 -1.97995674556033 -0.58745969373768 -1.1314038546059 -0.674490759476595 0.935583956693342 2.91554070225367 1.65359024903939 1.65359024903939 0.913826190258613 -0.565701927302951 -0.0870310657389155 -2.50214313999382 -0.913826190258613 -0.892068423823884 0.0652732993041866 -0.870310657389155 -0.961149332254148 0.0750000000000001 NA -2.425 -0.675 -1.58987107590912 -0.674490759476595 0.746757626563373 0.698579715172188 1.18579827069272 -0.50465495673069 0.8443265622225 1.13314447592068 1.45690004046945 0.0539592607581277 0.485633346823148 0.78240928099285 0.809388911371914 0.971266693646297 0.0539592607581277 1.268042627816 -0.620531498718468 0.917307432888169 1.10616484554162 2.02347227842979 0.350735194927829 -0.593551868339404 0.323755564548766 0.701470389855659 0.296775934169702 -1.40294077971132 -1.32200188857413 1.40294077971132 1.59179819236476 -2.69796303790638 2.05045190880885 -0.0269796303790638 -0.512612977202212 0.809388911371914 0.755429650613787 0.593551868339404 0.0539592607581277 0.377714825306893 -0.161877782274383 -0.458653716444085 0.78240928099285 -0.56657223796034 NA 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POSITION A C G T 1 0.866667 0.066667 0.066667 0 2 0 1 0 0 3 0 0 0.866667 0.133333 4 0.866667 0 0.133333 0 5 0 0.4 0 0.6 6 0 0 0.866667 0.133333 7 0.133333 0.6 0 0.266667 8 0 0.2 0.466667 0.333333 9 0.066667 0.333333 0.6 0 10 0 0 0.933333 0.066667 11 0.066667 0.933333 0 0

POSITION A C G T 1 1 0 0 0 2 0 0 0 1 3 0 0 0 1 4 0 0 0 1 5 1 0 0 0 6 0 0.5 0.5 0 7 0 1 0 0 8 1 0 0 0 9 0 0.5 0.5 0 10 0.5 0 0.5 0 11 0 0 0 1 12 0 0 0 1 13 0 0.5 0 0.5 14 0.5 0.5 0 0 15 0 0 0 1 16 0 0 0 1 17 1 0 0 0