GenExpdb_OKID Similarity2HmfAvsHmfAnb_upregulated_pgenes Similarity2HmfAvsHmfAnb_downregulated_pgenes GenExpdb_description_condition 28 -231.016222 -261.9114641 WT 5 min after 1 min UV treatment / WT 0 min before UV treatment 29 -61.54978086 -113.5562725 lexA 5 min after 1 min UV treatment / WT 0 min before UV treatment 30 -332.0968543 -294.0590009 WT 10 min after 1 min UV treatment / WT 0 min before UV treatment 31 -43.59688934 -96.75774208 lexA 10 min after 1 min UV treatment / WT 0 min before UV treatment 32 -308.8566256 -402.0123918 WT 20 min untreated cells / WT 0 min before UV treatment 33 -422.158033 -333.2544362 WT 20 min after 1 min UV treatment / WT 0 min before UV treatment 34 10.92887545 2.102471453 lexA 20 min untreated cells / WT 0 min before UV treatment 35 -61.78475508 -99.15153369 lexA 20 min after 1 min UV treatment / WT 0 min before UV treatment 36 -291.4904122 -187.9716209 WT 40 min after 1 min UV treatment / WT 0 min before UV treatment 37 -85.99386049 -123.0515116 lexA 40 min after 1 min UV treatment / WT 0 min before UV treatment 38 -314.1943734 -375.3782353 WT 60 min untreated cells / WT 0 min before UV treatment 39 -197.9534201 -162.6860039 WT 60 min after 1 min UV treatment / WT 0 min before UV treatment 40 -10.97572627 -3.050289028 lexA 60 min untreated cells / WT 0 min before UV treatment 41 -103.3279414 -119.8082761 lexA 60 min after 1 min UV treatment / WT 0 min before UV treatment 42 -1.563788471 -17.25317215 lexA 0 min before UV treatment / WT 0 min before UV treatment 43 3.987821106 159.0406828 10 min with 0.3 ug/ml mitomycin C / 0 min no MMC 44 93.77127445 108.1269203 25 min with 0.3 ug/ml mitomycin C / 0 min no MMC 45 85.94378284 107.4352353 40 min normal growth / 0 min normal growth 46 199.0473263 396.8752574 40 min with 0.3 ug/ml mitomycin C / 0 min no MMC 47 132.5602779 458.2136893 10 min exposure to 3.0 ug/ml mitomycin C followed by 50 min growth / 0 min no MMC 48 117.1624964 502.2647361 10 min exposure to 3.0 ug/ml mitomycin C followed by 70 min growth / 0 min no MMC 49 110.8876037 172.9739731 80 min normal growth / 0 min normal growth 50 125.1606195 175.9188975 80 min with 0.3 ug/ml mitomycin C / 0 min no MMC 54 -63.56689628 -23.48863444 appY Aerobic / WT Aerobic 55 -22.0512357 -17.13163022 arcA Aerobic / WT Aerobic 56 -19.03316566 10.18883826 arcA fnr Aerobic / WT Aerobic 57 63.0556273 37.19707858 fnr Aerobic / WT Aerobic 58 -20.21135794 48.89456506 oxyR Aerobic / WT Aerobic 59 -38.49574016 -22.43630279 soxS Aerobic / WT Aerobic 60 -163.6175675 -60.16100397 appY Anaerobic / WT Anaerobic 61 259.1262982 15.77825052 arcA Anaerobic / WT Anaerobic 62 435.0018345 133.9816036 arcA fnr Anaerobic / WT Anaerobic 63 157.3866026 58.67837307 fnr Anaerobic / WT Anaerobic 64 -15.93653228 -25.57805299 oxyR Anaerobic / WT Anaerobic 65 -159.421708 -87.55800004 soxS Anaerobic / WT Anaerobic 66 -89.03071023 9.160206469 Anaerobic WT / Aerobic WT 67 -97.05611726 39.57531988 MG1655 + F-plasmid / MG1655 68 123.2046553 353.1314509 DH5-alpha + F-plasmid / DH5-alpha 69 -49.0108071 -78.77108107 melR* / melR mutant 70 -165.1245207 469.3940288 mRNA abundance WT on LB / Genomic DNA from dnaC(ts) mutant 71 119.5180259 -516.1515795 mRNA abundance WT on LB / Genomic DNA from dnaC(ts) mutant (dye swap) 72 298.5715901 -342.4726148 mRNA abundance gyrA D82G mutant on LB / Genomic DNA from dnaC(ts) mutant 73 171.1605523 -378.6714651 mRNA abundance gyrA D82G mutant on LB / Genomic DNA from dnaC(ts) mutant (dye swap) 74 43.94648486 -307.8940767 "mRNA abundance (wt in LB, norfloxacin for 10 min) / Genomic DNA from dnaC(ts) mutant" 75 103.60478 -312.2401979 "mRNA abundance (wt in LB, norfloxacin for 10 min) / Genomic DNA from dnaC(ts) mutant (dye swap)" 76 274.893841 -422.801576 "mRNA abundance (wt in LB, norfloxacin for 30 min) / Genomic DNA from dnaC(ts) mutant" 77 198.8948718 -335.9874745 "mRNA abundance (wt in LB, norfloxacin for 30 min) / Genomic DNA from dnaC(ts) mutant (dye swap)" 78 -20.05727273 61.27866599 "mRNA abundance (gyrA D82G, LB) / mRNA abundance (wt, LB)" 79 12.02529241 -57.44614189 "mRNA abundance (gyrA D82G, LB) / mRNA abundance (wt, LB) (dye swap)" 80 6.016508409 25.75029502 "mRNA abundance (wt, M9) / Genomic DNA from dnaC(ts) mutant" 81 -25.8135495 190.7739296 2mM copper / no added copper 82 -108.9516807 -348.3116742 0.75mM added copper / no added copper 83 10.98550606 -31.56753923 no added copper / no added copper 84 24.77489386 51.19507314 DM medium / LB medium 85 160.6782473 33.50509465 glycerol / glucose 86 30.60065397 -41.53633629 succinate / glucose 87 404.4946558 114.9011214 alanine / glucose 88 581.1092055 136.8960423 acetate / glucose 89 641.0517571 174.947102 proline / glucose 90 19.95041841 82.28206512 Aerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Chemostat 1) 91 62.84098243 1.794284064 Aerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Chemostat 1 dye swap) 92 156.9457221 112.0682707 Aerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Chemostat 2) 93 63.17126298 75.61057217 Aerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Chemostat 2 dye swap) 94 -33.75425459 27.06833168 SAnaerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Run 1) 95 -89.80599914 164.1156358 Anaerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Run 1 dye swap) 96 -30.23984698 76.32138711 Anaerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Run 2) 97 -48.02718626 58.86799931 Anaerobic steady-state 200uM GSNO for 5 minutes / No GSNO (Run 2 dye swap) 98 10.47710874 157.4408783 5 min sigma32 induction / Control 99 -112.4465069 239.5565413 10 min sigma32 induction / Control 100 -148.4348754 248.3380246 15 min sigma32 induction / Control 101 21.28586026 142.3819603 IS5 deletion / WT Motile strain 102 -16.48618222 -152.8865314 IS5 deletion / WT Non-motile strain 103 -88.72907505 -403.1590493 WT Non-motile strain / WT Motile strain 104 -86.76352255 439.2053889 PHMB exposed / unexposed 105 7.713753675 -207.6437675 dam / WT 106 40.68404759 -86.03894255 dam mutS / WT 107 52.17702712 -65.73627554 mutS / WT 108 -97.53333022 -401.8046475 dam / WT 109 -88.02164469 -271.5775817 dam mutS / WT 110 14.35461844 -263.2124989 mutS / WT 111 -178.856942 -254.1885492 "dam mutS, cisplatin treated / WT cisplatin treated" 112 -289.5935939 -361.3411945 "dam, cisplatin treated / WT cisplatin treated" 113 160.9104588 -46.12449062 "mutS, cisplatin treated / WT cisplatin treated" 114 -63.27076651 14.99451475 WT pBAD-ryhB / WT pNM12 control 115 -10.11515979 -10.34526397 fur pBAD-ryhB / fur pNM12 control 116 -48.09689598 76.6342027 WT pBAD-ryhB +FeSO4 + / WT pNM12 control +FeSO4 117 -262.3066353 -77.83645606 rne pRNG3 / WT pPM30 118 -226.6823687 182.3448042 rne pNRNE5 / WT pPM30 119 -5.816455174 -64.12857581 rng / WT pPM30 Trial A 120 -137.4736425 -114.6460995 rne pBADRNE / WT pPM30 121 -9.547238464 -67.88684729 WT pRNG3 / WT pPM30 122 39.38870853 8.711886802 rng / WT pPM30 Trial B 123 -196.5711717 -203.9623817 rne pBAD-RNE without Arabinose / WT 159 25.78182893 -3.136671756 WT + Leu / WT - Leu 160 203.2792791 162.6456198 lrp + Leu / WT - Leu 161 181.5498085 172.5443878 lrp - Leu / WT - Leu 162 68.83310407 43.23612081 lrp + Leu / lrp - Leu 163 -88.94162045 -9.96014936 RpoE induced (2.5 min) / Wild type control (2.5 min) Expt 3 164 -9.41211304 -234.1883038 RpoE induced (2.5 min) / Wild type control (2.5 min) Expt 4 165 -2.441914806 91.7598544 RpoE induced (5 min) / Wild type control (5 min) Expt 1 166 -12.14993675 -1.741526927 RpoE induced (5 min) / Wild type control (5 min) Expt 2 167 -13.57715118 -40.55861981 RpoE induced (5 min) / Wild type control (5 min) Expt 3 168 -70.062138 -244.6450034 RpoE induced (5 min) / Wild type control (5 min) Expt 4 169 -81.62734385 -137.0180459 RpoE induced (10 min) / Wild type control (10 min) Expt 3 170 -58.28220904 -228.6152923 RpoE induced (10 min) / Wild type control (10 min) Expt 4 171 12.29498813 -48.62001596 RpoE induced (15 min) / Wild type control (15 min) Expt 1 172 -51.48844244 -83.87707512 RpoE induced (15 min) / Wild type control (15 min) Expt 2 173 -65.89557204 -24.04116772 RpoE induced (20 min) / Wild type control (20 min) Expt 3 174 -42.68806551 127.3857963 RpoE induced (20 min) / Wild type control (20 min) Expt 4 175 -45.8694667 -46.16472142 RpoE induced (30 min) / Wild type control (30 min) Expt 2 176 -71.27260386 -111.806079 RpoE induced (30 min) / Wild type control (30 min) Expt 3 177 -92.54021536 -89.22484229 RpoE induced (60 min) / Wild type control (60 min) Expt 3 178 -10.79213826 -215.2868763 RpoE induced (30 min) / Wild type control (30 min) Expt 4 179 10.36972428 18.44452729 RpoE induced (60 min) / Wild type control (60 min) Expt 1 180 -63.40237427 -20.36301145 RpoE induced (60 min) / Wild type control (60 min) Expt 2 181 -156.4746547 -349.8379124 RpoE induced (60 min) / Wild type control (60 min) Expt 4 182 5.313019537 -59.0456072 RpoE induced (0 min) / Wild type control (0 min) Expt 3 183 -22.15506693 -85.15908341 RpoE induced (0 min) / Wild type control (0 min) Expt 4 184 -193.0341662 142.9116409 ydgG / WT 185 20.36194214 279.0722899 fnr- aerobic / aerobic reference 186 -22.81903159 -113.6463888 WT aerobic / aerobic reference 187 401.8316536 341.2291205 fnr- anaerobic / aerobic reference 188 88.18521901 -80.53361757 WT anaerobic / aerobic reference 189 552.4613287 566.5041055 fnr- anaerobic + NO2 / aerobic reference 190 88.89333419 -89.73060718 WT anaerobic + NO2 / aerobic reference 191 301.8094262 418.1621299 fnr- anaerobic + NO3 / aerobic reference 192 86.39070357 -91.45807556 WT anaerobic + NO3 / aerobic reference 193 -122.4671696 97.79146326 fnr- aerobic / anaerobic reference 194 -257.9163154 -138.0624454 WT aerobic / anaerobic reference 195 125.963548 390.2517666 fnr- anaerobic / anaerobic reference 196 -97.61076834 -42.53275558 WT anaerobic / anaerobic reference 197 241.6650104 696.7395507 fnr- anaerobic + NO2 / anaerobic reference 198 -67.55198117 0.40854015 WT anaerobic + NO2 / anaerobic reference 199 136.0221202 382.7271745 fnr- anaerobic + NO3 / anaerobic reference 200 -115.7999064 -98.91162939 WT anaerobic + NO3 / anaerobic reference 201 44.85740681 -1.108166954 narXL anaerobic + NO2 / anaerobic reference 202 95.22513722 209.6831599 narXLP anaerobic + NO2 / anaerobic reference 203 31.02587186 162.8473196 WT 20 gL EtOH / WT 0 gL EtOH 204 85.79926832 291.5544635 WT 40 gL EtOH / WT 0 gL EtOH 205 -239.8176087 -114.8493523 WT biofilm after 7h of culturing / WT biofilm after 4h of culturing 206 -223.8603887 -84.60946683 WT after 7h of suspension culture / WT after 4h of suspension culture 207 -1.46582541 116.4600413 WT biofilm after 15h of culturing / WT biofilm after 4h of culturing 208 -153.7135749 58.66509594 WT after 15h of suspension culture / WT after 4h of suspension culture 209 -75.4251164 251.6568685 WT biofilm after 24h of culturing / WT biofilm after 4h of culturing 210 -184.5917825 320.1464442 WT after 24h of suspension culture / WT after 4h of suspension culture 211 -91.87352196 -48.93901758 WT biofilm after 4h of culturing / WT after 4h of suspension culture 212 -134.1093801 -65.52612148 WT biofilm after 7h of culturing / WT after 7h of suspension culture 213 51.92766951 40.38810202 WT biofilm after 15h of culturing / WT after 15h of suspension culture 214 -2.969718255 0.9407708 WT biofilm after 24h of culturing / WT after 24h of suspension culture 215 87.45826563 191.6112645 yceP biofilm / WT biofilm 216 -95.43098882 114.2118752 yliH biofilm / WT biofilm 217 6.122866981 39.6884281 dpiA overexpressor/ wt 218 -18.91122838 135.3021358 dpiA 2-fold overexpressor/ wt 219 72.98243859 85.80304367 RpoH induced (2.5 min) / Wild type control (2.5 min) 220 52.68041084 32.84233418 RpoH induced (5 min) / Wild type control (5 min) 221 23.15584701 4.010107227 RpoH induced (10 min) / Wild type control (10 min) 222 -37.43812033 -28.75708152 RpoH induced (20 min) / Wild type control (20 min) 223 99.95687431 105.9451399 RpoH induced (0 min) / Wild type control (0 min) 224 -93.50042826 -83.05806542 WT M9 2 min post rif / WT M9 225 -57.90595171 119.1642018 WT LB 2 min post rif / WT LB 226 -85.54893717 -29.11817676 WT M9 4 min post rif / WT M9 227 -24.50487241 251.6801666 WT LB 4 min post rif / WT LB 228 12.61011617 409.3682541 WT LB 6 min post rif / WT LB 229 -65.71565038 76.49297622 WT M9 6 min post rif / WT M9 230 -21.10236988 89.56284326 WT M9 8 min post rif / WT M9 231 35.94277542 543.9780443 WT LB 8 min post rif / WT LB 232 383.3125871 -2.274176738 WT LB / Genomic DNA 233 578.9333156 -123.4977338 WT M9-glucose / Genomic DNA 234 -60.07545943 -76.74976282 15 min after Ampicillin (100 ug/ml) / 0 min before treatment 235 -37.23791757 -22.27785256 30 min after Ampicillin (100 ug/ml) / 0 min before treatment 236 -19.36568203 -24.49304756 45 min after Ampicillin (100 ug/ml) / 0 min before treatment 237 7.627811892 -5.373310089 60 min after Ampicillin (100 ug/ml) / 0 min before treatment 238 2.082093229 -17.41521717 75 min after Ampicillin (100 ug/ml) / 0 min before treatment 239 -148.9060306 -171.917307 0 min after Ampicillin (100 ug/ml) / 0 min before treatment 240 40.46011927 93.43007115 2 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB 241 62.74878335 58.21278966 5 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB 242 52.09251728 23.74744535 10 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB 243 45.19114116 35.043419 20 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB 244 39.22751737 73.51900479 40 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB 245 33.71464383 76.54467749 60 min timepoint washed in 0.1 M CaCl2 + 15 % glycerol / before washing in LB 246 -550.9956907 -487.1130723 15 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5 247 -540.7782249 -527.0713869 30 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5 248 -472.6563493 -440.1823685 45 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5 249 -461.5534538 -492.2437127 60 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5 250 -355.3764528 -479.2316525 75 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5 251 -235.0736279 -132.4762827 90 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5 252 -92.12956117 142.8387509 0 min recovery from stationary phase LB + glucose / Bogel-Vonner OD 0.5 253 -1.493178392 156.6396251 5 min after Indol-acrylate (10 ug/ml) / 0 min before treatment 254 -26.43476799 132.9648594 15 min after Indol-acrylate (10 ug/ml) / 0 min before treatment 255 -130.1983112 -79.5357463 30 min after Indol-acrylate (10 ug/ml) / 0 min before treatment 256 -110.8947473 -206.1016195 60 min after Indol-acrylate (10 ug/ml) / 0 min before treatment 295 101.1931487 237.9661535 2 min after Norfloxacin (50 ug/ml) / 0 min before treatment 296 61.27087968 183.8634914 5 min after Norfloxacin (50 ug/ml) / 0 min before treatment 297 103.2489029 322.9471115 10 min after Norfloxacin (50 ug/ml) / 0 min before treatment 298 122.8095574 473.0264714 20 min after Norfloxacin (50 ug/ml) / 0 min before treatment 299 75.19325266 410.3919005 30 min after Norfloxacin (50 ug/ml) / 0 min before treatment 300 50.74233884 -132.3466844 gyrA parC 2 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment 301 -21.27665516 -268.382503 gyrA parC 5 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment 302 -3.754690015 -199.9906532 gyrA parC 10 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment 303 245.8098203 213.9117023 gyrA parC 20 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment 304 219.17075 275.6780798 gyrA parC 30 min after Norfloxacin (15 ug/ml) / gyrA parC 0 min before treatment 305 9.150948489 -169.4476185 gyrA parC 2 min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment 306 73.35010841 -37.69225762 gyrA parC 5 min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment 307 43.01389415 -130.9046272 gyrA parC 10 min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment 308 288.2099113 159.4185478 gyrA parC 20min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment 309 240.4244577 209.7780885 gyrA parC 30 min after Norfloxacin (50 ug/ml) / gyrA parC 0 min before treatment 310 385.5939159 737.5298229 15 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 311 446.0029938 821.597757 30 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 312 358.5733734 760.0874794 45min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 313 404.1018459 806.0105237 60 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 314 364.6311875 779.4706416 75 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 315 435.3035299 909.5272248 90 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 316 342.4238449 654.4573367 0 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 317 130.2435067 522.4282423 15 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 318 93.23727382 558.8372811 30 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 319 -5.922229074 490.1787394 45min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 320 0.481607497 548.5219898 60 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 321 -16.9818844 539.7507746 75 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 322 35.48345887 533.9284745 90 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 323 288.2738291 642.4741193 0 min recovery in 10mM Na-P / Bonner-Vogel OD~0.5 324 -47.21663683 -428.4955854 5 min 0.01 M Sodium Azide treatment / 0 min before treatment in Bonner-Vogel 325 -38.36305546 -343.368721 15 min 0.01 M Sodium Azide treatment / 0 min before treatment in Bonner-Vogel 326 -36.80295674 -438.3699331 30 min 0.01 M Sodium Azide treatment / 0 min before treatment in Bonner-Vogel 327 -43.96399129 -375.9549935 60 min 0.01 M Sodium Azide treatment / 0 min before treatment in Bonner-Vogel 328 44.84464532 -360.8317391 OD 0.03 anaerobic growth in M9 + glucose / genomic DNA reference 329 192.0625823 10.36340258 OD 0.2 anaerobic growth in M9 + glucose / genomic DNA reference 330 229.5182415 41.51216813 OD 0.35 anaerobic growth in M9 + glucose / genomic DNA reference 331 309.2268915 37.6109434 OD 0.6 anaerobic growth in M9 + glucose / genomic DNA reference 332 290.3261786 29.75175909 OD 0.9 anaerobic growth in M9 + glucose / genomic DNA reference 333 185.8988169 59.68079301 stationary phase anaerobic growth in M9 + glucose / genomic DNA reference 334 48.27478496 -213.2608467 OD 0.05 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference 335 97.1191619 -280.2878095 OD 0.21 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference 336 169.7721223 -152.8657074 OD 0.43 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference 337 132.5669556 -143.2661516 OD 0.7 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference 338 21.78185608 -42.32351512 OD 1.2 anaerobic growth in M9 + glucose + fumarate / genomic DNA reference 339 73.47097956 -68.35656514 stationary phase anaerobic growth in M9 + glucose + fumarate / genomic DNA reference 340 -167.223969 -343.6869672 Anaerobic growth in M9 + glucose OD 0.08 / Aerobic OD 0.4 341 -142.7219141 -360.2432403 Anaerobic growth in M9 + glucose OD 0.15 / Aerobic OD 0.4 342 -59.15931849 -199.6535566 Anaerobic growth in M9 + glucose OD 0.34 / Aerobic OD 0.4 343 11.17707971 -126.4147573 Anaerobic growth in M9 + glucose OD 0.73 / Aerobic OD 0.4 344 -5.992829641 -106.742909 Anaerobic growth in M9 + glucose OD 1.02 / Aerobic OD 0.4 345 -117.4630183 161.3218988 Anaerobic growth in M9 + glucose OD 1.27 / Aerobic OD 0.4 346 32.52326289 -160.8219439 Anaerobic growth in M9 + glucose + fumarate OD 0.15 / Aerobic OD 0.4 347 50.01244079 -208.5261399 Anaerobic growth in M9 + glucose + fumarate OD 0.30 / Aerobic OD 0.4 348 134.3160967 -65.94682647 Anaerobic growth in M9 + glucose + fumarate OD 0.63 / Aerobic OD 0.4 349 135.3471677 -61.3549538 Anaerobic growth in M9 + glucose + fumarate OD 0.85 / Aerobic OD 0.4 350 121.1251925 -52.78935973 Anaerobic growth in M9 + glucose + fumarate OD 1.07 / Aerobic OD 0.4 351 -135.2201942 219.196651 Anaerobic growth in M9 + glucose + fumarate OD 1.29 / Aerobic OD 0.4 352 100.8812529 130.5767712 5 min after Gamma treatment / 0 min before treatment 353 161.4976463 173.8693216 10 min after Gamma treatment / 0 min before treatment 354 131.2409383 96.07401481 20 min after Gamma treatment / 0 min before treatment 355 92.38955182 95.56175837 40 min after Gamma treatment / 0 min before treatment 356 84.29171279 37.66062022 60 min after Gamma treatment / 0 min before treatment 357 47.45429036 -89.17175316 acrD- 5 min after Novobiocin (5 ug/ml) / acrD- 0 min before treatment 358 38.41851112 -65.43440433 acrD- 5 min after Novobiocin (20 ug/ml) / acrD- 0 min before treatment 359 76.89514971 -112.4563397 acrD- 5 min after Novobiocin (50 ug/ml) / acrD- 0 min before treatment 360 47.95224379 7.613215138 acrD- 5 min after Novobiocin (200 ug/ml) / acrD- 0 min before treatment 361 178.7230024 121.9889722 DH5alpha OD 0.2 in LB + Amp pUC expression / DH5alpha OD 0.2 in LB no pUC 362 264.455306 470.1308367 DH5alpha OD 0.5 in LB + Amp pUC expression / DH5alpha OD 0.5 in LB no pUC 363 153.1835216 472.3360842 DH5alpha OD 0.9 in LB + Amp pUC expression / DH5alpha OD 0.9 in LB no pUC 364 245.3637454 5.67198672 MG1655 Stationary phase in LB OD 2.4 T1 / MG1655 genomic DNA 365 273.7616736 -65.41657038 MG1655 Stationary phase in LB OD 2.8 T2 / MG1655 genomic DNA 366 263.3902781 -33.00155107 MG1655 Stationary phase in LB OD 3.1 T3 / MG1655 genomic DNA 367 234.5810393 -9.091237732 MG1655 Stationary phase in LB OD 3.1 T4 (for 20 min) / MG1655 genomic DNA 368 214.4339838 -90.37547684 MG1655 Stationary phase in LB OD 3.1 T5 (for 40 min) / MG1655 genomic DNA 369 181.0423423 -16.72554983 MG1655 Stationary phase in LB OD 3.1 T6 (for 60 min) / MG1655 genomic DNA 370 -153.068291 14.68236161 rraA OD600=1.0 / WT OD600=1.0 371 -87.46270344 29.20491582 rraA OD600=0.3 / WT OD600=0.3 372 -37.48835125 55.72279031 rraA OD600=0.5 / WT OD600=0.5 373 -74.21586396 48.14300139 KSL2009 + pTrc99A-rraA (rraR overexpressing) / KSL2009 control 374 -50.73676789 -122.4346152 KSL2000 Rne depletion / KSL2000 control 375 288.7821855 161.4951985 KSL2009 N-Rne depletion / KSL2009 control 376 -247.3605075 -411.9572436 KSL2000 + pTrc99A-rraA (rraR overexpressing) / KSL2000 control 409 181.5853944 -6.293251617 WT Norfloxacin treated for 5 min / WT Nontreated at 0 min 410 117.854258 76.27920107 (recA-) Norfloxacin treated mutant for 5 min / (recA-) Nontreated mutant at 0 min 411 48.27256981 -54.71324275 (topA-) Norfloxacin treated mutant for 5 min / (topA-) Nontreated mutant at 0 min 412 -0.649600149 56.28421115 (dnaC) Norfloxacin treated mutant for 5 min / (dnaC) Nontreated mutant at 0 min 413 152.2449199 7.042927464 WT Norfloxacin treated for 10 min / WT Nontreated at 0 min 414 169.7002408 31.50912341 (recA-) Norfloxacin treated mutant for 10 min / (recA-) Nontreated mutant at 0 min 415 48.27677058 -47.68493999 (topA-) Norfloxacin treated mutant for 10 min / (topA-) Nontreated mutant at 0 min 416 33.55217965 44.1981272 (dnaC) Norfloxacin treated mutant for 10 min / (dnaC) Nontreated mutant at 0 min 417 168.2366282 -23.06056368 WT Norfloxacin treated for 15 min / WT Nontreated at 0 min 418 240.199282 151.0313754 (recA-) Norfloxacin treated mutant for 15 min / (recA-) Nontreated mutant at 0 min 419 59.89892856 -58.08649644 (topA-) Norfloxacin treated mutant for 15 min / (topA-) Nontreated mutant at 0 min 420 43.72354712 50.61249706 (dnaC) Norfloxacin treated mutant for 15 min / (dnaC) Nontreated mutant at 0 min 421 137.5602929 101.6801788 WT Norfloxacin treated for 20 min / WT Nontreated at 0 min 422 91.35759875 274.3118218 (recA-) Norfloxacin treated mutant for 20 min / (recA-) Nontreated mutant at 0 min 423 64.41196126 -46.02424474 (topA-) Norfloxacin treated mutant for 20 min / (topA-) Nontreated mutant at 0 min 424 68.62026714 95.89361303 (dnaC) Norfloxacin treated mutant for 20 min / (dnaC) Nontreated mutant at 0 min 425 46.17944912 -11.95487269 gyrB 2 min after upshift to 42 C / gyrB before upshift 426 113.7362054 176.9382269 gyrB 5 min after upshift to 42 C / gyrB before upshift 427 113.635606 205.3355988 gyrB 10 min after upshift to 42 C / gyrB before upshift 428 153.0136969 225.8686536 gyrB 20 min after upshift to 42 C / gyrB before upshift 429 122.7834615 120.394347 WT aerobic pH 5.0 / WT aerobic pH 7.0 430 55.65131497 263.855399 WT aerobic pH 8.7 / WT aerobic pH 7.0 431 304.5835258 223.0083751 WT anaerobic pH 5.0 / WT anaerobic pH 7.0 432 138.2156572 15.18312919 WT anaerobic pH 8.5 / WT anaerobic pH 7.0 433 28.54958582 2.286049779 yceP LB glu 24 hr biofilm cells + 0.06% DMF / WT LB glu 24 hr biofilm cells 434 -54.80158355 60.67370728 LB glu 24 hr biofilm cells + 600uM indole / WT LB glu 24 hr biofilm cells 435 -108.2089425 -46.03587283 trpE LB glu 24 hr biofilm cells / WT LB glu 24 hr biofilm cells 436 94.89802298 -152.9199356 WT LB 24 hr biofilm cells / WT LB glu 24 hr biofilm cells 437 -140.5702627 -116.1492779 tnaA LB glu 24 hr biofilm cells / WT LB glu 24 hr biofilm cells 438 -13.22306313 -73.00101362 UV Irradiated 50h / Not irradiated 439 -73.96821097 64.52267128 UV Irradiated 1h / Not irradiated 440 176.1679101 23.98116057 UV Irradiated 1h / Not irradiated: dye swap 441 32.7880698 9.693190865 continuous culture 40h / batch culture 40h 442 45.4810631 31.71630861 continuous culture 500h / batch culture 500h 443 23.86126958 89.31906372 WT + arginine(100 ug/ml) / WT in minimal medium 444 354.1320766 33.28351493 argR + arginine(100 ug/ml) / WT in minimal medium 445 40.83259815 86.26399951 Continuous culture no oxygen / 5 min exposure to oxygen 446 49.57120325 128.3890951 Continuous culture no oxygen / 10 min exposure to oxygen 447 34.10369812 69.43038702 Continuous culture no oxygen / 15 min exposure to oxygen 448 107.7793689 62.77037056 Continuous culture no oxygen / 60 min exposure to oxygen 449 148.851334 114.282882 WT at pH 5.5 for 1 min / WT at pH 7.6 450 408.8904785 393.9864264 WT at pH 5.5 for 5 min / WT at pH 7.6 451 421.8106619 256.8345979 WT at pH 5.5 for 10 min / WT at pH 7.6 452 43.13647646 -14.20898458 exponential growth phase + IAA solution 0.5 mM / exponential growth phase 453 31.81820003 -44.21145325 Aerobic wildtype 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wildtype control 454 -70.41381361 14.01585288 Aerobic wildtype 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wildtype control (dye swap) 455 81.9977274 125.6943113 Anaerobic wildtype 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture anaerobic wildtype control 456 -17.39380689 36.99559852 Anaerobic wildtype 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture anaerobic wildtype control (dye swap) 457 -147.5758768 31.36713736 Anaerobic norR 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture anaerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes 458 -98.19682019 -289.1258487 Anaerobic norR 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture anaerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes (dye swap) 459 -123.3245893 -236.7312081 Aerobic norR 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes 460 -198.5527461 -480.1328671 Aerobic norR 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes (dye swap) 461 -181.7002733 -61.31442186 Aerobic hmp 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes 462 -156.2246999 -319.4855734 Aerobic hmp 10 uM each NOC-5 and NOC-7 for 5 minutes / Continuous culture aerobic wild type 10 uM each NOC-5 and NOC-7 for 5 minutes (dye swap) 463 145.1133746 70.83705956 cueO + Fe(II) / WT + Fe(II) 464 39.45515144 8.686007843 BL21 (pOri1) (mu=0.39) / BL21 (mu=0.46) 465 38.07007954 22.13027922 BL21 (pOri2) (mu=0.29) / BL21 (mu=0.46) 466 23.08397219 -17.21537191 BL21 (pOri1) (mu=0.20) / BL21 (mu=0.20) 467 55.09501781 -21.70396981 BL21 (pOri2) (mu=0.20) / BL21 (mu=0.20) 468 -27.1490884 24.3521831 TPEN treated / untreated 469 -258.8871486 -86.62124959 TPEN treated / untreated; dye swap 473 -139.6662887 289.9083083 FliA / WT on MOPS glucose 474 369.27365 876.3427668 flhDC / WT on MOPS glucose 475 -108.4121669 -118.689109 FliA overexpression / empty pTet32 control 476 15.7395224 133.514307 ycfR LB glu biofilm culture for 15h / WT LB glu biofilm culture for 15h 477 145.6376976 44.95209358 WT + (HoxEFUYH [hydrogenase] ) / WT 478 -23.5617567 -7.265197649 Overproduced Rsd / control: OD 0.4 479 110.9405293 60.3726233 Overproduced Rsd / control: OD 0.9 480 138.3522677 50.52538796 Overproduced Rsd / control: OD 1.1 481 44.54466931 -9.814897797 Overproduced Rsd / control: Stationary phase 486 257.2200136 86.00815372 WT anaerobic LB 3h / WT anaerobic LB 2h30 487 253.6523894 266.9751294 UTI89 anaerobic LB 3h / UTI89 anaerobic LB 2h30 488 585.3249876 359.2670418 UTI89 anaerobic LB 3h30 / UTI89 anaerobic LB 2h30 489 358.9588526 484.1064419 WT anaerobic LB 3h45 / WT anaerobic LB 2h30 490 778.3791241 568.8391411 UTI89 anaerobic LB 4h / UTI89 anaerobic LB 2h30 491 316.2550337 466.3042048 WT anaerobic LB 4h30 / WT anaerobic LB 2h30 492 763.4167506 826.7224652 WT aerobic LB 5h / WT aerobic LB 2h30 493 702.5989244 469.3992128 UTI89 aerobic LB 5h / UTI89 aerobic LB 2h30 494 430.9487139 427.2905098 UTI89 anaerobic LB 6h / UTI89 anaerobic LB 2h30 495 186.2520366 468.5039927 WT anaerobic LB 6h45 / WT anaerobic LB 2h30 496 644.1796335 814.3150604 WT aerobic LB 8h / WT aerobic LB 2h30 497 597.9340954 796.2194899 WT aerobic LB 12h / WT aerobic LB 2h30 498 663.7806581 406.5456747 UTI89 aerobic LB 12h / UTI89 aerobic LB 2h30 499 659.7893218 858.6751086 WT aerobic LB 18h / WT aerobic LB 2h30 500 686.2253008 369.0357251 UTI89 aerobic LB 8h / UTI89 aerobic LB 2h30 501 663.9394845 600.3835098 UTI89 aerobic LB 19h30 / UTI89 aerobic LB 2h30 502 517.5899217 924.6618834 WT aerobic LB 26h / WT aerobic LB 2h30 503 371.3378709 603.1192375 UTI89 aerobic LB 26h / UTI89 aerobic LB 2h30 504 -124.4319572 6.434886406 UTI89 gnotobiotic cecum 14 day post-inoculation / MG1655 gnotobiotic cecum 14 day post-inoculation 505 50.00558545 36.23595074 rseA / WT (Exp 1) 506 3.642119874 -21.96751509 rseA / WT (Exp 2) 507 -12.276894 20.67770741 rseA / WT (Exp 3) 508 24.77163525 79.27991707 hfq / WT (Exp 1) 509 33.07909409 133.2498165 hfq / WT (Exp 2) 510 4.729147885 -35.74701148 rpoE overexpression 20 min / WT 511 -137.8622364 -404.6021479 Day 1 anaerobic WT / reference 512 -151.6660562 -124.6487853 Day 3 aerobic lon / reference 513 -80.02035109 -127.8347708 Day 1 anaerobic lon / reference 514 -259.769778 -307.4535926 Day 3 aerobic WT / reference 515 -86.70210127 -255.2712664 Day 1 aerobic WT / reference 516 -147.4345929 -427.7982992 Day 3 anaerobic lon / reference 517 24.48771751 -289.2951238 Day 1 aerobic lon / reference 518 -171.8228067 -375.2061258 Day 3 anaerobic WT / reference 519 27.12870766 38.99472002 5 min oxygen depletion / control with oxygen 520 -43.49694819 -37.68907143 10 min oxygen depletion / control with oxygen 521 -133.1131255 -72.83791283 15 min oxygen depletion / control with oxygen 522 -136.5084983 -58.44421065 60 min oxygen depletion / control with oxygen 523 244.7662399 31.90324498 Benzalkonium chloride adapted strain / control 524 318.3048281 1.546586482 Adapted strain with 50 ppm benzalkonium chloride / control 525 56.14452652 -10.85111599 NsrR- phenocopy + TMA + NO2 / control 526 -2.742345951 28.11849854 NsrR- phenocopy / control 527 56.91982512 108.9156985 NsrR+ TMA and NO2 / control 528 -127.7490073 -307.5689294 (dinI+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 529 -106.0181545 -330.4708486 (dinP+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 530 -91.88001334 -329.4893302 (lexA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 531 -126.1790825 -328.6722705 (lon+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 532 37.42282642 -35.3836301 (luc+) 0.025ug/ml norfloxacin / (luc+) without norfloxacin 533 -130.3550353 -338.807583 (luc+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 534 -210.2496134 -399.8248357 (mazF+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 535 -118.9224354 -364.9448454 (recA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 536 -250.5461796 -402.9230155 (relE+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 537 -112.7444145 -309.3542623 (ruvA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 538 -114.5481698 -332.129495 (sulA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 539 -99.51936966 -339.934415 (umuD+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 540 -111.3508663 -318.1527029 (uvrA+) 0.025ug/ml norfloxacin / WT 0.025ug/ml norfloxacin 541 -194.2699085 -129.1477752 (yebF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 542 235.3583924 77.62049474 (luc+) 0.075ug/ml norfloxacin / (luc+) without norfloxacin 543 -185.646772 -118.5597572 (zipA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 544 -77.79930563 -46.56734132 (yfjF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 545 -113.849198 -51.34746939 (bcp+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 546 -139.3515937 -47.05786103 (cpxR+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 547 -104.1416029 -43.72334804 (crcB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 548 -87.46240405 -55.95591577 (crp+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 549 -83.69973547 -83.0086397 (cspF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 550 -136.8096458 -134.3370941 (dam+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 551 -149.7856179 -58.68317396 (dnaA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 552 -102.6233616 -85.15744966 (dnaN+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 553 -128.2719757 -91.13629658 (dnaT+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 554 -203.7584233 -166.1152079 (emrR+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 555 -98.80505214 -38.26148195 (era+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 556 -69.65053068 -37.86111286 (fis+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 557 -92.51092636 -2.370369152 (fklB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 558 -107.9865516 -60.40027477 (folA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 559 -140.4208301 -78.63049587 (galF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 560 -121.8004901 -77.59247532 (gcvR+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 561 -105.5016711 -85.58161408 (gyrA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 562 -162.8698744 -117.0071241 (gyrI+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 563 -168.4259765 -122.2007685 (hlpA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 564 -166.7679024 -145.8090323 (holD+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 565 -201.9197111 -161.2416778 (hscA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 566 -201.000071 -173.6721007 (IHF+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 567 -76.37970465 -40.58446711 (idrA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 568 -69.25216077 -51.57650243 (mcrB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 569 -85.73731448 -22.20438745 (mcrC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 570 -163.8688658 -75.74593468 (menB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 571 -181.6739442 -103.4047541 (menC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 572 -171.2346618 -77.36224748 (minD+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 573 -181.7775769 -132.6579476 (minE+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 574 -178.6337949 -145.9650372 (murI+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 575 -406.443637 -273.0856057 (yoeB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 576 -163.9271258 -155.0470317 (nrdA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 577 -176.288429 -165.7051156 (nrdB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 578 -122.1839029 -87.17243701 (nupC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 579 -101.7567378 -10.16248968 (pyrC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 580 -146.6106452 -82.21726726 (rimI+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 581 -195.4649396 -129.5613593 (rstB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 582 -120.6785876 -118.8084025 (ruvC+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 583 -193.3804618 -117.8245128 (sbcB+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 584 -188.8667491 -116.440386 (uspA+) 0.075ug/ml norfloxacin / WT 0.075ug/ml norfloxacin 585 15.58478501 -66.86069495 WT with 0.025 ug/ml norfloxacin / WT without norfloxacin 586 -47.01651439 -51.70133722 WT with 0.050 ug/ml norfloxacin / WT without norfloxacin 587 204.9455356 -188.0918445 WT with 0.075 ug/ml norfloxacin / WT without norfloxacin 588 62.00692625 -129.690175 (recA-) / WT 589 -42.26383429 -74.75005859 (recA-) 0.075ug/ml norfloxacin / (recA-) without norfloxacin 590 -19.95873666 -14.07985609 (recA-) 1.0ug/ml norfloxacin / (recA-) without norfloxacin 591 448.4729174 -1.500888098 WT with 1.0 ug/ml norfloxacin / WT without norfloxacin 592 53.16725001 8.006016862 luciferase + 0.025ug/ml norfloxacin / luciferase 593 -2.95417387 45.00271147 WT 12 min after 0.025 ug/ml norfloxacin / WT prior to treatment 594 203.5526083 122.7571659 WT 24 min after 0.025 ug/ml norfloxacin / WT prior to treatment 595 239.3113615 82.93739798 WT untreated cells after 24 min / WT prior to treatment 596 330.9794247 217.1820968 WT 36 min after 0.025 ug/ml norfloxacin / WT prior to treatment 597 290.4930639 227.7857705 WT 48 min after 0.025 ug/ml norfloxacin / WT prior to treatment 598 302.4912627 213.7330126 WT 60 min after 0.025 ug/ml norfloxacin / WT prior to treatment 599 357.1516462 252.7118815 WT untreated cells after 60 min / WT prior to treatment 600 -108.2017243 -87.96692205 (ccdB+) 30 min after induction / (ccdB+) 0 min after induction 601 -112.2379915 28.28759406 (ccdB+) 60 min after induction / (ccdB+) 0 min after induction 602 -37.56757738 117.7240404 (ccdB+) 90 min after induction / (ccdB+) 0 min after induction 603 93.05823881 176.2752076 (ccdB+) 120 min after induction / (ccdB+) 0 min after induction 604 1.688837999 27.42692995 (lacZ+) 30 min after induction / (lacZ+) 0 min after induction 605 167.2836731 82.59514488 (lacZ+) 60 min after induction / (lacZ+) 0 min after induction 606 311.7376928 106.3377616 (lacZ+) 90 min after induction / (lacZ+) 0 min after induction 607 231.6719347 61.88859074 (lacZ+) 120 min after induction / (lacZ+) 0 min after induction 608 -94.08838311 -614.4563641 (lacZ+ recA-) 0 min after induction / (lacZ+) 0 min after induction 609 -46.41002759 30.00687861 (lacZ+ recA-) 30 min after induction / (lacZ+ recA-) 0 min after induction 610 -1.409673685 76.02818201 (lacZ+ recA-) 60 min after induction / (lacZ+ recA-) 0 min after induction 611 33.34397822 153.3635857 (lacZ+ recA-) 90 min after induction / (lacZ+ recA-) 0 min after induction 612 -167.0197419 -715.1021346 (ccdB+ recA-) 0 min after induction / (ccdB+) 0 min after induction 613 -114.4516985 30.18690128 (ccdB+ recA-) 30 min after induction / (ccdB+ recA-) 0 min after induction 614 -71.0731597 270.651989 (ccdB+ recA-) 60 min after induction / (ccdB+ recA-) 0 min after induction 615 -130.0501727 381.0885099 (ccdB+ recA-) 90 min after induction / (ccdB+ recA-) 0 min after induction 616 3.426854685 -493.9067891 (lacZ+) W1863 (lambda-) 0 min after induction / (lacZ+) 0 min after induction 617 26.53490541 2.84162869 (lacZ+) W1863 (lambda-) 30 min after induction / (lacZ+) W1863 (lambda-) 0 min after induction 618 175.8151632 169.8470849 (lacZ+) W1863 (lambda-) 60 min after induction / (lacZ+) W1863 (lambda-) 0 min after induction 619 333.027004 488.5302879 (lacZ+) W1863 (lambda-) 90 min after induction / (lacZ+) W1863 (lambda-) 0 min after induction 620 17.51386827 -560.3485089 (ccdB+) W1863 (lambda-) 0 min after induction / (ccdB+) 0 min after induction 621 59.76655273 63.6217167 (ccdB+) W1863 (lambda-) 30 min after induction / (ccdB+) W1863 (lambda-) 0 min after induction 622 457.4746464 383.9700007 (ccdB+) W1863 (lambda-) 60 min after induction / (ccdB+) 0 min after induction 623 699.631016 559.8829568 (ccdB+) W1863 (lambda-) 90 min after induction / (ccdB+) 0 min after induction 624 115.491964 144.3915795 (lacZ+ recA-) 120 min after induction / (lacZ+ recA-) 0 min after induction 625 -263.0621375 356.7456771 (ccdB+ recA-) 120 min after induction / (ccdB+ recA-) 0 min after induction 626 42.1245707 -36.48676792 EMG2 LB + 0.2% glucose 3h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation 627 57.55419163 -35.32426405 EMG2 LB + 0.2% glucose 3.5h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation 628 146.0730309 -5.065955301 EMG2 LB + 0.2% glucose 4h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation 629 214.5448483 37.97943805 EMG2 LB + 0.2% glucose 4.5h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation 630 301.8317338 444.0039447 EMG2 LB + 0.2% glucose 5h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation 631 466.9867869 427.2564217 EMG2 LB + 0.2% glucose 5.5h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation 632 504.0867333 523.7584931 EMG2 LB + 0.2% glucose 6h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation 633 503.0051268 290.2624542 EMG2 LB + 0.2% glucose 8h post-incubation / EMG2 LB + 0.2% glucose 2.5h post-incubation 634 9.956384784 1.206879385 EMG2 LB + 0.4% glucose 3h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation 635 141.3302419 66.14763326 EMG2 LB + 0.4% glucose 3.5h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation 636 366.6428165 180.266938 EMG2 LB + 0.4% glucose 4h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation 637 371.3360852 333.2342848 EMG2 LB + 0.4% glucose 4.5h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation 638 546.464972 552.9063817 EMG2 LB + 0.4% glucose 5h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation 639 519.7252046 563.07033 EMG2 LB + 0.4% glucose 5.5h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation 640 459.6381116 558.886602 EMG2 LB + 0.4% glucose 6h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation 641 327.8223652 578.1371366 EMG2 LB + 0.4% glucose 8h post-incubation / EMG2 LB + 0.4% glucose 2.5h post-incubation 642 61.73539213 -148.212414 ATCC25404 with pR1drd19 24h in LB / ATCC25404 without R1drd19 24h in LB 643 29.51812319 65.83344825 MG1655 with pR1drd19 24h in M9C glu / MG1655 without pR1drd19 24h in M9C glu 644 199.7745157 286.833209 BW25113 with pR1drd19 24h in LB / BW25113 with pR1drd19 7h in LB 645 16.46054476 68.83963343 BW25113 with pR1drd19 24h in LB / BW25113 without pR1drd19 24h in LB 646 287.5812821 227.8625347 BW25113 with pR1drd19 15h in LB / BW25113 with pR1drd19 7h in LB 647 123.5287346 83.30252894 BW25113 15h in LB / BW25113 7h in LB 648 82.66867536 48.24724 BW25113 24h in LB / BW25113 7h in LB 649 -34.57350429 38.1541341 ymgB / WT biofilm on LB 24 h 650 85.5350584 66.58765663 soxR 2 min paraquat treatment / (soxR) before paraquat treatment 651 -47.91957108 -14.96019882 WT 2 min paraquat treatment / WT before paraquat treatment 652 219.5315503 56.46944028 soxR 4 min paraquat treatment / (soxR) before paraquat treatment 653 64.52712144 -24.43972019 WT 4 min paraquat treatment / WT before paraquat treatment 654 121.9476437 -40.08684965 soxR 6 min paraquat treatment / (soxR) before paraquat treatment 655 36.82700097 -57.83390488 WT 6 min paraquat treatment / WT before paraquat treatment 656 115.3848979 -20.99568218 soxR 8 min paraquat treatment / (soxR) before paraquat treatment 657 74.74949344 -87.86547867 WT 8 min paraquat treatment / WT before paraquat treatment 658 172.2490171 55.66045911 soxR 10 min paraquat treatment / (soxR) before paraquat treatment 659 40.36367712 -124.6774791 WT 10 min paraquat treatment / WT before paraquat treatment 660 -37.68304744 -415.7374506 phoU mutant / WT reference 661 111.5957113 -136.9412803 WT tp1: 780 min / WT tp1: 780 min 662 51.14524392 -86.37725221 WT tp2: 830 min / WT tp1: 780 min 663 48.80903682 -130.5048528 WT tp3: 861 min / WT tp1: 780 min 664 92.03843787 87.96099576 WT tp4: 869 min / WT tp1: 780 min 665 218.5408443 223.4080214 WT tp5: 878 min / WT tp1: 780 min 666 274.493746 228.2209799 WT tp6: 888 min / WT tp1: 780 min 667 263.4743164 144.4601689 WT tp7: 898 min / WT tp1: 780 min 668 211.5872428 14.47900345 WT tp8: 908 min / WT tp1: 780 min 669 159.3025707 -84.34152347 WT tp9: 919 min / WT tp1: 780 min 670 93.62856797 -8.085581207 WT tp10: 929 min / WT tp1: 780 min 671 46.21378 -0.8964461 WT tp11: 939 min / WT tp1: 780 min 672 59.81090829 -90.45721559 WT tp12: 969 min / WT tp1: 780 min 673 103.1459077 -66.08957181 WT tp13: 999 min / WT tp1: 780 min 674 -10.77464909 193.1004392 WT tp14: 1035 min / WT tp1: 780 min 675 156.3042423 259.6236012 WT tp15: 1049 min / WT tp1: 780 min 676 285.9496168 313.41083 WT tp16: 1070 min / WT tp1: 780 min 677 154.7138839 291.4964033 WT tp17: 1089 min / WT tp1: 780 min 678 28.44823623 -54.44154734 rpoS tp1: 120 min / WT tp1: 780 min 679 12.69779615 -71.83760635 rpoS tp2: 150 min / WT tp1: 780 min 680 -79.39916507 81.82144223 rpoS tp3: 160 min / WT tp1: 780 min 681 60.16134173 167.5072472 rpoS tp4: 170 min / WT tp1: 780 min 682 24.37864091 298.6772889 rpoS tp5: 180 min / WT tp1: 780 min 683 130.0368428 149.7367397 rpoS tp6: 190 min / WT tp1: 780 min 684 80.07205503 77.70874167 rpoS tp7: 200 min / WT tp1: 780 min 685 100.9676435 -87.61603405 rpoS tp8: 210 min / WT tp1: 780 min 686 -9.107361054 -0.501398491 rpoS tp9: 220 min / WT tp1: 780 min 687 -25.74447998 -18.28578296 rpoS tp10: 250 min / WT tp1: 780 min 688 -56.66853606 51.58760918 rpoS tp11: 290 min / WT tp1: 780 min 689 -91.93584476 89.90529116 rpoS tp12: 315 min / WT tp1: 780 min 690 -40.04208274 138.2010212 rpoS tp13: 330 min / WT tp1: 780 min 691 321.6314538 -120.9858662 crp tp2: 250 min / WT tp1: 780 min 692 119.5369994 181.881955 crp tp5: 405 min / WT tp1: 780 min 693 203.339672 151.6475022 crp tp6: 420 min / WT tp1: 780 min 694 153.0896546 114.3377928 crp tp7: 450 min / WT tp1: 780 min 695 174.9896074 -31.0741363 relA tp1: 832 min / WT tp1: 780 min 696 98.20319781 9.504046077 relA tp2: 865 min / WT tp1: 780 min 697 46.10028233 5.363958318 relA tp4: 896 min / WT tp1: 780 min 698 166.3162617 59.88361701 relA tp5: 909 min / WT tp1: 780 min 699 225.2453734 69.79347421 relA tp6: 916 min / WT tp1: 780 min 700 224.3980918 146.2311974 relA tp7: 925 min / WT tp1: 780 min 701 272.9801227 203.1426532 relA tp8: 935 min / WT tp1: 780 min 702 199.6512741 150.8440693 relA tp9: 945 min / WT tp1: 780 min 703 52.85427129 192.4690007 relA tp10: 955 min / WT tp1: 780 min 704 53.12896333 104.7252631 relA tp11: 966 min / WT tp1: 780 min 705 0.574586406 -342.962474 "PaeR7I r+m+ pTN9, 0 h / PaeR7I r-m+ pTN11, 0 h" 706 -89.56582222 -25.6596282 "PaeR7I r+m+ pTN9, 1 h / PaeR7I r-m+ pTN11, 1 h; Rep1" 707 86.81705756 -455.2228012 "PaeR7I r+m+ pTN9, 1 h / PaeR7I r-m+ pTN11, 1 h; Rep2" 708 197.7562097 8.54276424 "PaeR7I r+m+ pTN9, 1 h 50 m / PaeR7I r-m+ pTN11, 1 h 50 m" 709 485.990852 449.6310772 "PaeR7I r+m+ pTN9, 3 h / PaeR7I r-m+ pTN11, 3 h" 710 -408.7520055 345.7441342 90 min fis / WT 711 -73.03301609 315.5232491 150 min fis / WT 712 300.945305 185.1509879 240 min fis / WT 713 20.52639338 -70.92677938 360 min fis / WT 727 -21.73357022 -69.18741626 argR +NO / argR untreated (expt 1) 728 -45.96450167 -86.63201397 argR +NO / argR untreated (expt 2) 729 55.07123173 217.890723 WT +serine hydroxamate / WT untreated 730 116.9916163 162.4106662 ArcA +NO / ArcA untreated 731 -0.668730549 -49.74553941 WT +degraded DeaNO / WT untreated 732 12.03950994 23.12465385 iscR +NO / iscR untreated 733 84.51358716 309.7561442 metJ +NO / metJ untreated (expt 1) 734 74.34867012 221.6764789 metJ +NO / metJ untreated (expt 2) 735 32.61796971 186.8703829 norR +NO / norR untreated (expt 1) 736 21.06475242 75.20279412 norR +NO / norR untreated (expt 2) 737 -8.588468006 -15.53235139 nsrR +NO / nsrR untreated 738 72.74908173 77.83452603 nsrR hmpA +NO / nsrR hmpA untreated (expt 1) 739 -17.68433018 366.1771857 nsrR hmpA +NO / nsrR hmpA untreated (expt 2) 740 84.1705811 41.14146294 WT +NO / WT untreated (diff platform) 741 94.19422136 188.9314678 WT +NO / WT untreated 742 32.99729466 221.6100317 WT +NO / WT untreated (dye swap) 743 -32.23170934 82.49475654 WT +met +NO / WT untreated 744 10.87897131 -210.5812203 E. coli NCM3722 + 0.3 M NaCl / E. coli NCM3722 control; 30 degrees 745 -12.15629477 -76.35444352 E. coli NCM3722 + 0.3 M NaCl + 1mM glycine betaine / E. coli NCM3722 control; 30 degrees 746 -164.458661 -160.3816329 E. coli NCM3722 + 0.3 M NaCl / E. coli NCM3722 control; 43 degrees 747 -134.9003266 -56.53421974 E. coli NCM3722 + 0.3 M NaCl + 1mM glycine betaine / E. coli NCM3722 control; 43 degrees 748 -87.67900026 -286.1255589 rpoS biofilm / WT biofilm 749 -98.97123481 281.7083587 WT biofilm / WT exponential 750 91.06000454 -25.16165007 rpoS exponential / WT exponential 751 423.8003261 915.5620168 WT stationary phase / WT exponential 752 -331.6587787 -563.5599482 rpoS stationary / WT stationary 753 105.3337029 128.1324074 0 min aerobic to anaerobic shift / control 754 -24.52892044 195.8672167 2 min aerobic to anaerobic shift / control 755 35.77876329 215.9780561 5 min aerobic to anaerobic shift / control 756 38.39076519 287.4889642 15 min aerobic to anaerobic shift / control 757 444.6908311 586.0393785 25 min Rep 1 aerobic to anaerobic shift / control 758 397.3176389 681.762939 25 min Rep 2 aerobic to anaerobic shift / control 759 237.076789 482.0324757 35 min aerobic to anaerobic shift / control 760 199.3390193 319.5758626 45 min aerobic to anaerobic shift / control 761 209.7175892 490.8766905 55 min Rep 1 aerobic to anaerobic shift / control 762 298.8987002 547.0718298 55 min Rep 2 aerobic to anaerobic shift / control 763 -210.7507023 -181.5506221 pck overexpression early log phase / WT early log phase 764 -291.6074339 -260.0532544 ppc overexpression early log phase / early log phase 765 -157.8580934 -209.3286729 ppc overexpression chemostat / WT chemostat 766 -137.6823299 -237.9758637 pck overexpression chemostat / WT chemostat 767 -69.98177169 31.0442887 WT +DPTA / WT untreated (expt 1) 768 28.34199767 23.72138023 WT +DPTA / WT untreated (expt 2) 769 -59.5658108 -65.58227553 cysB +500uM GSNO / cysB untreated 770 91.67533431 198.1554568 nsrR +500uM GSNO / nsrR untreated 771 119.1567972 214.7761772 flhDC +500uM GSNO / flhDC untreated (expt 1) 772 8.012566833 70.79405227 WT +met +500uM GSNO / WT +met untreated (expt 2) 773 96.80150353 149.7230278 WT +cys +500uM GSNO / WT +cys untreated 774 81.71043878 196.3693899 flhDC +500uM GSNO / flhDC untreated (expt 2) 775 95.36995665 280.9887999 WT +100uM GSNO / WT untreated 776 80.5189708 210.4616085 WT +100uM GSNO / WT untreated (dye swap) 777 19.47457466 73.66541829 dpp +100uM GSNO / dpp untreated 778 110.6878173 234.9955482 WT +500uM GSNO / WT untreated 779 0.646601513 62.92980339 WT +met +500uM GSNO / WT +met untreated (expt 1) 780 17.19807989 40.7470582 metJ +500uM GSNO / metJ untreated 781 3.934396484 53.07835884 metJ +500uM GSNO / metJ untreated (dye swap) 782 50.26491059 -94.18572495 yncC biofilm cells / wt biofilm cells 783 3.425670082 -41.87869776 yncC colony / wt colony 784 105.9342214 13.47781642 4h LB biofilm hha / WT 785 93.47361213 10.47732815 4h LB-glu biofilm hha / WT 786 40.64442433 -24.27396153 15h LB-glu biofilm hha / WT 787 47.27183921 -28.64654995 24h LB-glu biofilm hha / WT 788 64.60757526 21.64097716 S TP1 / A TP1 789 286.4050624 -195.6720416 L TP1 / A TP1 790 -23.87033771 -265.2955979 S TP2 / A TP2 791 -16.37709694 24.65054872 L TP2 / A TP2 792 35.51392689 36.42307811 S TP3 / A TP3 793 75.75345711 19.0720563 L TP3 / A TP3 794 39.37079549 17.63527135 S TP4 / A TP4 795 92.61056233 10.42070781 L TP4 / A TP4 797 354.4533981 -10.80893841 23 degrees C / 37 degrees C 798 4.483405227 60.04244737 lsrR / W3110 wild-type 799 25.3814908 -1.523424655 lsrK / W3110 wild-type 804 -217.6729488 263.9562351 L-threonine producing strain / W3110 lacI (pKK223-3) control 806 -9.361151262 -12.87815699 luxS in LB / WT W3110 in LB 807 72.3755457 45.28972455 luxS in LB + 0.8% glucose / WT W3110 in LB + 0.8% glucose 824 43.04288174 177.2309283 1% tannin / continuous culture without tannin 825 79.7215268 -227.7049351 rpoS / WT 826 53.49605143 -174.9133684 sdiA free-living cells 30 degrees / WT free-living cells 30 degrees 827 12.96433038 9.650012018 luxS free-living cells +AI-2 30 degrees / luxS free-living cells without AI-2 30 degrees 828 122.4062852 167.9114722 luxS free-living cells +AI-2 37 degrees / luxS free-living cells without AI-2 30 degrees 829 2.534515446 -117.4359629 luxS free-living cells +AI-2 37 degrees / luxS free-living cells without AI-2 37 degrees 830 13.42503284 21.26881756 tnaA biofilm +100 uM indole 30 degrees / tnaA biofilm without indole 30 degrees 831 -90.76398898 -152.273101 tnaA biofilm +100 uM indole 37 degrees / tnaA biofilm without indole 37 degrees 832 120.1357236 -62.96427931 WT biofilm cells 30 degrees / WT free-living cells 30 degrees 833 100.5346133 20.47797713 sdiA with biofilm cells +1mM indole 30 degrees / sdiA biofilm cells without indole 30 degrees 834 41.57328695 -80.44262706 hha overexpression / control 835 -34.24100385 -17.77985083 10 ug cefsulodin -5 min / untreated -5 min 836 -12.40068006 -0.01487709 0.03 ug mecillinam -5 min / untreated -5 min 837 30.05710591 7.102229134 10 ug cefsulodin and 0.03 ug mecillinam -5 min / untreated -5 min 838 -29.13482171 -18.63302813 10 ug cefsulodin 5 min / untreated 5 min 839 7.159627423 -2.064447713 0.03 ug mecillinam 5 min / untreated 5 min 840 42.7521048 14.6623545 10 ug cefsulodin and 0.03 ug mecillinam 5 min / untreated 5 min 841 -67.73550321 -104.2066405 60 ug cefsulodin 5 min / untreated 5 min 842 83.95595694 39.59392222 60 ug cefsulodin 10 min / untreated 10 min 843 65.03938413 71.50237155 10 ug cefsulodin 20 min / untreated 20 min 844 4.73945934 -19.15494879 0.03 ug mecillinam 20 min / untreated 20 min 845 12.03110796 26.44533879 10 ug cefsulodin and 0.03 ug mecillinam 20 min / untreated 20 min 846 -137.4981243 4.780418069 60 ug cefsulodin 20 min / untreated 10 min 847 -32.55003734 -41.17479046 10 ug cefsulodin 40 min / untreated 40 min 848 -9.922438764 25.58493182 0.03 ug mecillinam 40 min / untreated 40 min 849 86.36915925 65.68628783 10 ug cefsulodin and 0.03 ug mecillinam 40 min / untreated 40 min 850 -64.94229288 137.1865718 60 ug cefsulodin and 0.3 ug mecillinam 40 min / untreated 40 min 851 -50.75329073 99.79537633 0.3 ug mecillinam 60 min / untreated 60 min 852 -59.88069805 -120.7858114 batch culture control / (T2) glucose limited fed-batch (dye swap) 853 158.1825376 46.27908375 (T2) glucose limited fed-batch / batch culture control 854 -107.6424634 -103.1195507 batch culture control / (T3) glucose limited fed-batch (dye swap) 855 102.8962415 64.44432727 (T3) glucose limited fed-batch / batch culture control 856 -60.73773291 -107.9096766 batch culture control / (T4) glucose limited fed-batch (dye swap) 857 135.1469487 43.44374219 (T4) glucose limited fed-batch / batch culture control 858 -64.14039344 -150.6491906 batch culture control / (T5) glucose limited fed-batch (dye swap) 859 58.84363045 96.9209624 (T5) glucose limited fed-batch / batch culture control 860 -54.46846141 -151.2316124 batch culture control / (T6) glucose limited fed-batch (dye swap) 861 119.6768704 106.5498725 (T6) glucose limited fed-batch / batch culture control 862 -86.11234361 -131.1799227 batch culture control / (T7) glucose limited fed-batch (dye swap) 863 107.6327924 69.80898715 (T7) glucose limited fed-batch / batch culture control 864 -55.33904815 -169.3104352 batch culture control / (T8) glucose limited fed-batch (dye swap) 865 172.3121322 64.95832634 (T8) glucose limited fed-batch / batch culture control 866 -9.183530309 -12.15811523 batch culture control / (T1) glucose limited fed-batch (dye swap) 867 5.296436976 9.982067167 (T1) glucose limited fed-batch / batch culture control 872 90.43807142 29.24721113 MG1655 10 ug bicyclomycin / MG1655 control 873 75.32226564 49.27802024 MG1655 25 ug bicyclomycin / MG1655 control 874 -39.2586034 270.0342886 MG1655 100 ug bicyclomycin / MG1655 control 875 56.36451462 209.1017864 O157:H7 100 ug bicyclomycin / O157:H7 control 876 74.00372202 190.3318354 MDS42 100 ug bicyclomycin / MDS42 control 877 -8.854818987 155.4231465 MDS42 nusA / MDS42 control 878 198.8541883 225.2151285 MDS42 nusG / MDS42 control 907 50.10408928 92.28466621 E. coli B178 groESL(-) expressing human Hsp60 and Hsp10 / E. coli B178 groESL(-) expressing human wt and Val98Ile Hsp60 and Hsp10 908 3.343087819 272.7920931 4.5% NaCl in TSB / pooled RNA control 909 -336.0311209 -115.5188266 15% glycerol in TSB / pooled RNA control 910 28.70939519 63.25956007 HCl (pH 4.75) in TSB / pooled RNA control 911 -309.8048611 47.89527163 NaOH (pH 9.6) in TSB / pooled RNA control 912 -334.6158354 75.86895508 0.05 M acetate in TSB / pooled RNA control 913 -95.73358672 155.5859102 Heat (46o) in TSB / pooled RNA control 914 -176.4459262 193.9359801 5% ethanol in TSB / pooled RNA control 915 33.39230125 110.6674078 Cold (15o) in TSB / pooled RNA control 916 -351.1111892 -77.27382655 7 ppm benzalkonium Cl in TSB / pooled RNA control 917 -372.4732123 -97.2056209 9 ppm benzalkonium Cl in TSB / pooled RNA control 918 -33.07049161 123.9669334 150 mg/ml ethidium Br in TSB / pooled RNA control 925 -79.44088088 400.5655735 relA spoT isoleucine starved / WT replete isoleucine 926 -114.7314137 558.7404789 relA isoleucine starved / WT replete isoleucine 927 716.6896896 1211.913121 WT isoleucine starved / WT replete isoleucine 928 560.8747307 1477.309097 crp isoleucine starved / WT replete isoleucine 929 59.9646135 965.6081997 dksA isoleucine starved / WT replete isoleucine 930 558.7645453 1462.833783 lrp isoleucine starved / WT replete isoleucine 931 431.476355 1188.61491 rpoS isoleucine starved / WT replete isoleucine 932 -285.2101973 -23.29051709 rpoS isoleucine starved / WT isoleucine starved 933 95.42135114 134.0832672 WT isoleucine starved tp 1 / WT replete isoleucine 934 103.9461133 133.2667493 WT isoleucine starved tp 2 / WT replete isoleucine 935 392.6762778 108.5656001 WT isoleucine starved tp 3 / WT replete isoleucine 936 144.1488181 196.5179556 WT isoleucine starved tp 4 / WT replete isoleucine 937 195.3748635 415.6001914 WT isoleucine starved tp 5/ WT replete isoleucine 938 232.6172316 453.2481513 WT isoleucine starved tp 6 / WT replete isoleucine 939 416.1463362 536.5488119 WT isoleucine starved tp 7 / WT replete isoleucine 940 390.1761578 754.0356255 WT isoleucine starved tp 8 / WT replete isoleucine 941 453.391679 892.8746512 WT isoleucine starved tp 9 / WT replete isoleucine 942 492.9171096 1199.391332 WT isoleucine starved tp 10 / WT replete isoleucine 943 621.0439168 1263.687768 WT isoleucine starved tp 11 / WT replete isoleucine 944 636.4992137 1501.357505 WT isoleucine starved tp 12 / WT replete isoleucine 945 746.4947526 492.6505261 WT stationary phase / WT exponential phase 946 84.56455755 42.63843151 hupA / WT LB exponential 947 -99.07351863 -2.361699681 hupA / WT LB transition 948 -43.7428511 45.01810111 hupA / WT LB stationary 949 -60.66485831 87.62028743 hupB / WT LB exponential 950 55.20436995 6.550773954 hupB / WT LB transition 951 126.879061 29.83181574 hupB / WT LB stationary 952 59.3420043 -11.30593227 hupAB / WT LB exponential 953 -171.3066462 -117.8769749 hupAB / WT LB transition 954 -68.26343164 -146.9389792 hupAB / WT LB stationary 955 16.05753431 -49.6543288 rpoS / WT LB exponential 956 -508.8551665 19.08717221 rpoS / WT LB stationary 957 -534.3491326 -263.2680281 hupAB / WT M9 glucose exponential 958 -384.7739655 -137.5635317 hupAB / WT M9 glycerol exponential 959 -42.1151256 91.52183889 hupAB / WT M9 glucose stationary 960 71.07207243 462.8212555 hupAB / WT M9 glycerol stationary 967 -699.4954043 915.7569264 WT 100 mM Cd(II) for 10 min / WT 968 -388.5397155 747.5905022 gshA 100 mM Cd(II) for 10 min / WT 969 -319.8833057 1192.430466 gshB 100 mM Cd(II) for 10 min / WT 970 -657.8598701 -476.6313506 sdiA overexpression / empty vector control 971 -254.0789131 -142.075109 sdiA1E11 overexpression / empty vector control 972 -49.31438544 71.87305913 zinc limited chemostat / control 973 23.48670665 -13.89704734 zinc limited chemostat / control (dye swap) 975 -27.12418479 -39.49752894 mazEF relBEF chpB yefM-yoeB dinJ-yafQ / MG1655 WT biofilm cells on LB 976 133.7697672 298.375112 15 min oxygen downshift / control 977 84.45183907 576.5417879 45 min oxygen downshift / control 978 278.4933375 767.7885179 75 min oxygen downshift / control 979 45.73541683 166.1063703 sucrose / control on min glucose 980 11.85777718 -19.37921495 NaCl / control on min glucose 986 -96.41020768 82.32959857 5 min no Cd pH 7 / 5 min no Cd pH 5 (dye swap) 989 112.9852268 168.1105443 Generation 50 LB + 10% cranberry juice / LB 990 70.37463125 222.0782178 Generation 160 LB + 10% cranberry juice / LB 991 -117.7944242 -20.37837762 Generation 210 LB + 10% cranberry juice / LB 992 193.5791448 156.7094586 Generation 230 LB + 10% cranberry juice / LB 993 64.84840856 -43.97942314 yjgK / WT control biofilm 994 -5.102854442 -77.08269593 5FU / control biofilm 995 347.5685805 442.2186239 WT stationary phase / WT exponential phase 996 -100.2346687 -796.2757442 rpoS / WT M63 glucose exponential 997 -213.3345644 122.2973493 rpoS / WT M63 glucose stationary 1004 -160.897457 34.65674111 30 uM CO-RMs 15 min / aerobic control 1005 -221.9112269 -17.03801431 30 uM CO-RMs 15 min / aerobic control (dye swap) 1006 -43.57910814 45.78343123 100 uM CO-RMs 15 min / anaerobic control 1007 -87.55709006 -45.78705792 100 uM CO-RMs 15 min / anaerobic control (dye swap) 1016 -433.7785665 307.2536243 attachment stage biofilm / colony stage biofilm 1017 -453.8197628 12.33460239 attachment stage biofilm / maturation stage biofilm 1018 -418.9122273 -88.61581333 attachment stage biofilm /planktonic exponential phase 1019 16.70834029 -395.8961219 colony stage biofilm /planktonic exponential phase 1020 37.69834697 -100.9685513 maturation stage biofilm /planktonic exponential phase 1021 515.4524853 -2070.806452 planktonic exponential phase / planktonic stationary phase 1022 69.4215129 525.8526523 wildtype 1% isobutanol / wildtype 1023 34.04375898 503.5775417 wildtype 1% butanol / wildtype 1024 138.2132424 437.9796945 wildtype 3% ethanol / wildtype 1025 143.1453752 715.5837302 ihfA 1% isobutanol / ihfA 1026 135.4518561 340.0825894 fur 1% isobutanol / fur 1027 355.1475687 606.9419277 phoB 1% isobutanol / phoB 1028 283.835202 582.018121 arcA 1% isobutanol / arcA 1029 272.6592404 552.9805863 ubiE1% isobutanol / ubiE 1032 616.5437306 -358.5327373 biofilm outside / biofilm inside 1033 -754.2567959 -1402.68153 Planktonic exponential phase / Planktonic stationary phase 1034 288.345813 -202.7342013 biofilm inside / Planktonic exponential phase 1035 -14.19263619 111.2976403 biofilm outside / Planktonic exponential phase 1036 -76.27503287 2.497552694 rpoS- / WT 1037 63.95255069 464.8837765 evolved rpoS+ (DMS1735) / WT 1038 144.1940493 95.85301347 evolved rpoS+ (DMS1737) / WT 1039 274.8117793 199.8769 evolved rpoS+ (DMS1739) / WT 1040 -12.18394845 85.69916328 evolved rpoS+ (DMS1741) / WT 1041 194.0984348 240.7187234 evolved rpoS+ (DMS1743) / WT 1042 -134.3118239 27.39561263 evolved rpoS- (DMS1745) / rpoS- (DMS1688) 1043 -10.0123737 -33.65660045 evolved rpoS- (DMS1747) / rpoS- (DMS1688) 1044 -223.1730103 -184.7791248 evolved rpoS- (DMS1749) / rpoS- (DMS1688) 1045 -104.0154797 -63.35208175 evolved rpoS- (DMS1751) / rpoS- (DMS1688) 1046 -0.115611381 -16.42107519 evolved rpoS- (DMS1753) / rpoS- (DMS1688) 1047 66.37575241 -51.05444867 "TOM-Green/IsoILR1/GSHI, cis-DCE / non-cloned genes, cis-DCE" 1048 101.9508558 28.22463818 "TOM-Green/EchA F108L/I219L/C248I, cis-DCE / TOM-Green, cis-DCE" 1049 261.1809874 360.5920536 "BW25113, H2O2 / BW25113, water" 1050 319.9973761 92.06561446 "BW25113 ygiW, H2O2 / BW25113 ygiW, water" 1051 192.0583477 307.1139908 "BW25113 ychH, H2O2 / BW25113 ychH, water" 1052 -177.6784127 -144.439315 UV irradiation (50 J/m2) / unirradiated 1053 -95.08188139 -158.9767779 FhlA133 (mutated) / FhlA (control) 1054 -5.935514293 -98.31871538 CORM-2 treated_anaerobic / anaerobic control 1055 -54.73698481 151.2636949 CORM-2 treated_aerobic / aerobic control 1056 -254.2463117 -202.4034799 BW25113 ompA/pCA24N ompA / BW25113 ompA/pCA24N control 1057 1.657887834 29.35369378 ompA / wt (polystyrene biofilm) 1058 -62.77699504 55.6325863 ompA / wt (glasswool biofilm) 1062 54.11334552 71.31756042 BW25113-mqsR / control 1063 182.6856226 -20.42901995 BW25113/pCA24N-mqsR / control (IPTG) 1064 -65.37081474 7.017493068 BW25113/pCA24N-mqsR / control (IPTG for 15 min) 1065 -174.9960667 320.5666956 "BW25113/pCA24N-mqsR / control (DNA, IPTG)" 1066 113.2519622 105.2757355 "BW25113/pBAD-mqsA / control (DNA, IPTG)" 1070 -133.6900742 -130.6066624 CP4-57-deficient / wild type 1078 -426.5480501 -938.3809319 triclosan / control 1080 323.8605776 36.49804102 wt GraL / wt control (short term) 1081 -153.8588844 261.8168526 ppGpp0 GraL / ppGpp0 control (short term) 1082 85.78182104 10.23656572 wt GraL / wt control (long term) 1083 168.1056212 -87.4924956 ppGpp0 GraL / ppGpp0 control (long term) 1084 36.13611383 54.74175832 adenosine 1085 -3.399572468 -9.342488108 alanine 1086 48.57590517 61.9462047 arginine 1087 45.15540042 71.27036276 aspartate 1088 71.0882731 121.22817 cysteine 1089 -42.9184889 -20.05947547 cytidine 1090 16.50738931 32.23120077 glutamate 1091 -41.50366497 -13.67605843 glutamine 1092 17.86237556 -30.47096404 glycine 1093 63.26016242 62.02679778 guanosine 1094 18.16448002 49.39882998 histidine 1095 53.88900493 130.5024382 isoleucine 1096 0.788953235 29.92433068 lysine 1097 -52.58649134 -59.41280646 methionine 1098 18.55790082 65.66581489 phenylalanine 1099 -25.82578562 -99.25223857 proline 1100 5.392240976 72.71800764 serine 1101 -1.013907397 -9.784935895 threonine 1102 -18.00437053 18.75751359 thymidine 1103 46.27383217 -14.86199902 tryptophan 1104 -52.15761255 -48.28643031 uridine 1105 32.62321661 -8.144687581 valine 1106 -22.69061248 3.713381227 del27 / WT 1107 -28.75193937 83.1489379 eBOP42 / WT 1108 -14.17142826 87.94120709 eBOP43 / WT 1113 195.1164038 511.3702779 heat shock 45 degrees 10 min / WT log phase 1114 917.8263433 993.0215976 stationary phase / log phase 1115 436.0429758 591.9364576 WT nitrogen-limited medium log phase / WT complete medium log phase 1132 87.36031057 -45.98311101 ada vs. wildtype 1133 119.6520638 -28.899096 wt + MMS / wt - MMS ( .5 h ) 1134 135.9792372 -44.24962356 wt + MMS / wt - MMS ( 1.5 h ) 1135 248.593142 -312.196725 wt + MMS / wt - MMS ( 3.9 h ) 1136 1270.493575 -796.7921375 ada + MMS / ada - MMS ( .5 h ) 1137 -84.08143199 -67.27232982 ada + MMS / ada - MMS ( 1.5 h ) 1138 130.473254 -167.7034769 ada + MMS / ada - MMS ( 3.9 h ) 1140 -56.8933702 -116.5876897 "0 min, butanol / unstressed" 1141 95.81226576 200.7666667 "30 min, butanol / unstressed" 1142 39.11192954 -65.72021651 "80 min, butanol / unstressed" 1143 43.92876149 -13.72833918 "195 min, butanol / unstressed" 1151 208.2472726 232.4219421 NTG-treated / control ( - triclosan) 1152 283.83958 268.5825087 NTG-treated / control ( + triclosan) 1155 -10.64211313 -58.40845377 Recombinant T1 / Recombinant T0 1156 -147.0322095 51.29621703 Recombinant T4 / Recombinant T0 1157 -116.6333157 114.7737617 Recombinant T1 + IPTG / Recombinant T0 1158 -171.4902416 93.21929912 Recombinant T4 + IPTG / Recombinant T0 1159 -46.35493541 -63.39238844 wt T1 / wt T0 1160 -8.071759786 -103.6208335 wt T4 / wt T0 1161 -34.20609683 -62.32188198 wt T1 + IPTG / wt T0 1162 -34.61324807 -59.40675025 wt T4 + IPTG / wt T0 1163 95.68918912 6.852789296 serine hydroxamate T1 / recombinant T0 1164 -111.5545362 68.55840763 Heat-Shocked 15 min / Recombinant T0 1165 -206.8402405 21.02888595 Heat-Shocked 15 min + IPTG / Recombinant T0 1171 466.5632378 43.43055695 Crp* + Glucose / WT + Glucose 1172 317.4164876 119.4165492 Crp* / WT 1173 260.186086 392.5160763 LY180 + furfural / LY180 1174 175.9608392 264.3675182 EMFR9 + furfural / EMFR9 1175 -22.47822137 -44.70656922 LY180 del yqhC / LY180 1176 36.81155064 50.54736212 LY180 furfural / LY180 1177 74.33994218 55.12645683 LY180 del yqhC furfural / LY180 del yqhC 1178 10.98742906 -33.19315098 LY180 del yqhC furfural / LY180 furfural 1179 -913.2711675 -704.5097956 "E. coli DST160, tolerant to high succinic acid concentration / E. coli W3110 WT" 1181 -139.0998858 -170.3961621 Biofilm / Planktonic 1182 -68.21602707 -105.0344602 CHIR-090 / DMSO control 1183 -289.5868861 -89.20685391 hfq deletion / wt 1184 -384.9116893 -97.95391551 mgrR - / wt 1185 -1.913464011 79.76921667 plasmid mgrR / plasmid control 1186 -10.43309573 -35.51823541 peroxynitrite / control 1187 -32.59706243 -46.79185146 hydrogen peroxide / control 1188 -43.30091492 -145.8864817 pFnrS / plasmid control 1189 -452.0966194 -641.4304953 Wild-type Cells / pooled reference RNA 1190 -68.53053453 1598.58309 SHX-treated WT / pooled reference RNA 1191 -183.1446816 114.0357784 Delta dksA Cells / pooled reference RNA 1192 -823.8771838 741.196427 SHX-treated Delta dksA Cells / pooled reference RNA 1193 -204.7253073 47.09539619 reuterin / control 1195 -315.7863179 427.4796206 thymine limited - 15 / control - 0 1196 -188.645564 438.4432078 thymine limited - 30 / control - 0 1197 109.7303623 -127.9250945 thymine limited - 45 / control - 0 1198 75.33764027 14.91521028 thymine limited - 60 / control - 0 1199 -8.598248464 100.4694555 thymine limited - 90 / control - 0 1200 -59.94706791 84.79315892 thymineless - 15 / control - 0 1201 -1.412257569 193.3037504 thymineless - 30 / control - 0 1202 -106.1304456 225.7986122 thymineless - 45 / control - 0 1203 23.41636285 179.4444367 thymineless - 60 / control - 0 1204 157.4331397 50.34347403 thymineless - 90 / control - 0 1206 -115.4098601 -45.22024012 rpoS mutants / WT 1207 41.36303318 91.79823215 rpoN mutants / WT 1208 7.702095658 -12.34533878 cold stress T1 / control T1 1209 -85.85257029 -80.73108429 cold stress T2 / control T2 1210 -234.2490017 -365.1446237 cold stress T3 / control T3 1211 -379.8046509 -449.6877047 cold stress T4 / control T4 1212 -367.2024961 -519.5725982 cold stress T5 / control T5 1213 -402.8734109 -518.9400253 cold stress T6 / control T6 1214 -460.3872095 -506.4105301 cold stress T7 / control T7 1215 -143.7560894 153.1933572 cold stress T8 / control T8 1216 31.48078536 14.62691649 heat stress T1 / control T1 1217 -43.34697921 -33.26745889 heat stress T2 / control T2 1218 201.5348548 1138.049667 heat stress T3 / control T3 1219 213.408196 1136.303617 heat stress T4 / control T4 1220 394.3451992 1327.497364 heat stress T5 / control T5 1221 289.8396966 1287.521646 heat stress T6 / control T6 1222 355.2057264 465.5586675 heat stress T7 / control T7 1223 281.7208994 1308.609892 heat stress T8 / control T8 1224 74.12892673 29.78290734 oxidative stress T1 / control T1 1225 -3.340867269 -91.20903664 oxidative stress T2 / control T2 1226 160.0411821 -23.52548218 oxidative stress T3 / control T3 1227 264.7614664 540.3957334 oxidative stress T4 / control T4 1228 283.2513332 597.17187 oxidative stress T5 / control T5 1229 119.3884496 532.4119404 oxidative stress T6 / control T6 1230 180.1082031 612.7279219 oxidative stress T7 / control T7 1231 175.1571584 1.058127709 oxidative stress T8 / control T8 1232 384.6181167 276.9104989 glucose-lactose shift T2 / control T2 1233 435.6910593 635.1155324 glucose-lactose shift T3 / control T3 1234 556.4354932 745.6232243 glucose-lactose shift T4 / control T4 1235 1415.752786 984.3172646 glucose-lactose shift T5 / control T5 1236 1285.120652 746.9339445 glucose-lactose shift T6 / control T6 1237 1380.645043 728.7481727 glucose-lactose shift T7 / control T7 1238 -27.06385658 -0.429898531 NADH Oxidase / Reference 1239 -18.94865112 -0.04269437 ATPase / Reference 1252 179.8403958 123.2326777 EHEC DMEM QseD / EHEC DMEM WT 1253 -147.5200929 -1024.592987 K-12 DMEM QseD / K-12 DMEM WT 1254 -117.9042807 -922.1903397 K-12 LB QseD / K-12 LB WT 1255 -73.71291834 -184.2559331 luxS deletion / WT 1256 63.13621628 -158.7923648 HG228 / MG1655 1257 31.46318704 58.57030819 E. coli mutant aerobic / WT anaerobic 1258 46.48687996 46.06670049 E. coli mutant aerobic / WT aerobic 1259 145.7670994 274.2481298 clpV deleted mutant / Wild Type 1260 61.15938462 261.1149424 hcp deleted mutant / Wild Type 1261 136.0935643 555.2237778 icmF deleted mutant / Wild Type 1262 69.70841653 -359.0245544 ldhA pflB mutated / wild type 1263 -19.58735604 -8.648685445 nusA11 mutant / WT 1264 23.49534463 21.41887505 T2 exposed norfloxacin and indole / T0 exposed norfloxacin 1265 31.61576787 10.10152624 T3 reexposed norfloxacin / T0 exposed norfloxacin 1273 116.9066722 29.65176171 ptsN mutant / WT 1282 185.4189951 -57.82395737 "pSpoT / pBRplac ,control" 1283 -15.80078171 406.6166086 MG1655star on glucose / WT on glucose 1284 8.321405207 477.7268397 flhD on glucose / WT on glucose 1285 -14.49242153 422.3636777 MG1655star on mannose / WT on mannose 1286 70.19769785 486.3595364 flhD on mannose / WT on mannose 1287 79.59916719 421.8272054 MG1655star A600=0.2 mucus / WT A600=0.2 mucus 1288 139.5544592 448.6938282 flhD A600=0.2 mucus / WT A600=0.2 mucus 1289 118.4057793 296.2318642 MG1655star A600=0.5 mucus / WT A600=0.5 mucus 1290 62.68793301 345.5168137 flhD A600=0.5 mucus / WT A600=0.5 mucus log2.fold_change._Fis_vs_WT -268.016653 296.4652179 NA log2.fold_change._Hns_vs_WT 868.7947732 -33.49080172 NA log2FoldChangeExpAEV 2449.470935 1710.602904 NA log2FoldChangeExpAmA 3153.922882 3269.821278 NA log2FoldChangeExpBEV 1789.531576 1328.903086 NA log2FoldChangeExpBmB 2147.029308 2381.501652 NA log2FoldChangemAEV -790.1277049 -1628.193389 NA log2FoldChangemBEV -447.2407192 -1122.355884 NA log2FoldChangeStatAEV 1718.775852 1473.102744 NA log2FoldChangeStatAmA 2079.785165 3244.872511 NA log2FoldChangeStatBEV.x 816.0334867 993.0031713 NA log2FoldChangeStatBEV.y 816.0334867 993.0031713 NA log2FoldChangeStatBmB 1158.303466 1553.216592 NA wt.on_ko.on_log2_fold_change 4.656480971 -77.69773189 NA