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Table 1 List of samples

From: Archetypal analysis of diverse Pseudomonas aeruginosatranscriptomes reveals adaptation in cystic fibrosis airways

Sample # Sample name Study Patient Clone Year Mucoid Mutator State1 Medium2 OD3
[1,2] Huse_A1 Study 1 A “A” ~1983 No N/A Early SCFSM 0.4-0.5
[3,4] Huse_A2 Study 1 A “A” ~1984 No N/A Early SCFSM 0.4-0.5
[5,6] Huse_A3.1 (m) Study 1 A “A” ~1985 Yes N/A Early SCFSM 0.4-0.5
[7,8] Huse_A3.2 Study 1 A “A” ~1985 No N/A Early SCFSM 0.4-0.5
[9,10] Huse_A4 (m) Study 1 A “A” ~1986 Yes N/A Early SCFSM 0.4-0.5
[11,12] Huse_B1 Study 1 B “B” ~1983 No N/A Early SCFSM 0.4-0.5
[13,14] Huse_B2.1 Study 1 B “B” ~1987 No N/A Late SCFSM 0.4-0.5
[15,16] Huse_B2.2 Study 1 B “B” ~1987 No N/A Late SCFSM 0.4-0.5
[17,18] Huse_B2.3 (m) Study 1 B “B” ~1987 Yes N/A Late SCFSM 0.4-0.5
[19,20] Huse_B3.1 (m) Study 1 B “B” ~1991 Yes N/A Late SCFSM 0.4-0.5
[21,22] Huse_B3.2 Study 1 B “B” ~1991 No N/A Late SCFSM 0.4-0.5
[23,24] Huse_B3.3 (m) Study 1 B “B” ~1991 Yes N/A Late SCFSM 0.4-0.5
[25,26] Huse_Ca1 Study 1 C “Ca” ~1983 No N/A Early SCFSM 0.4-0.5
[27,28] Huse_Ca2 (m) Study 1 C “Ca” ~1983 Yes N/A Early SCFSM 0.4-0.5
[29,30] Huse_Cb1 (m) Study 1 C “Cb” ~1987 Yes N/A Early SCFSM 0.4-0.5
[31,32] Huse_Cb2 Study 1 C “Cb” ~1987 No N/A Late SCFSM 0.4-0.5
[33,34] Huse_Cb3 (m) Study 1 C “Cb” ~1987 Yes N/A Late SCFSM 0.4-0.5
[35-36] Huse_PA14 Study 1 N/A “PA14” N/A No N/A wt SCFSM 0.4-0.5
[37-38] Huse_PAO1 Study 1 N/A “PAO1” N/A No N/A wt SCFSM 0.4-0.5
[39-41] Yang_PAO1 Study 2 N/A “PAO1” N/A No N/A wt LB 0.5
[42-47] Yang_CF510-2006 Study 2 N/A “WTB” N/A No N/A N/A LB 0.5
[48-50] Yang_B6.0 Study 2 B6 “B6” ~2005 No N/A Early LB 0.5
[51-53] Yang_B6.4 Study 2 B6 “B6” ~2007 No N/A Early LB 0.5
[54-56] Yang_B12.0 Study 2 B12 “B12” ~2005 No N/A Early LB 0.5
[57-59] Yang_B12.4 Study 2 B12 “B12” ~2007 No N/A Early LB 0.5
[60-62] Yang_B12.7 Study 2 B12 “B12” ~2009 No N/A Early LB 0.5
[63-65] Yang_B38.1 Study 2 B38 “B38” ~2005 No N/A Early LB 0.5
[66-68] Yang_B38.2 (m) Study 2 B38 “B38” N/A Yes N/A Early LB 0.5
[69-71] Yang_B38.2 Study 2 B38 “B38” ~2005 No N/A Early LB 0.5
[72-74] Yang_B38.6 (m) Study 2 B38 “B38” ~2006 Yes N/A Early LB 0.5
[75-77] Yang_CF43-1973 Study 2 CF43 “DK2” 1973 No N/A Early LB 0.5
[78-80] Yang_CF66-1973 Study 2 CF66 “DK2” 1973 No N/A Late LB 0.5
[81-83] Yang_CF105_1973 Study 2 CF105 “DK2” 1973 No N/A Early LB 0.5
[84-86] Yang_CF114_1973 Study 2 CF114 “DK2” 1973 No N/A Early LB 0.5
[87-89] Yang_CF30-1979 Study 2 CF30 “DK2” 1979 No N/A Late LB 0.5
[90-92] Yang_CF173-1984 Study 2 CF173 ”DK2” 1984 No N/A Late LB 0.5
[93-95] Yang_CF333-1991 Study 2 CF333 ”DK2” 1991 No N/A Late LB 0.5
[96-98] Yang_CF66-1992 Study 2 CF66 “DK2” 1992 No N/A Late LB 0.5
[99-101] Yang_CF333_1997 Study 2 CF333 “DK2” 1997 No N/A Late LB 0.5
[102-104] Yang_CF173-2002 Study 2 CF173 “DK2” 2002 No N/A Late LB 0.5
[105-107] Yang_CF243-2002 Study 2 CF243 “DK2” 2002 No N/A Late LB 0.5
[108-110] Yang_CF333-2003 Study 2 CF333 “DK2” 2003 No N/A Late LB 0.5
[111-113] Yang_CF173-2005 Study 2 CF173 “DK2” 2005 No N/A Late LB 0.5
[114-116] Yang_CF333-2005 Study 2 CF333 “DK2” 2005 No N/A Late LB 0.5
[117-119] Yang_CF333-2007.1 Study 2 CF333 “DK2” 2007 No N/A Late LB 0.5
[120-122] Yang_CF333-2007.2 (m) Study 2 CF333 “DK2” 2007 Yes N/A Late LB 0.5
[123-125] Yang_CF333-2007.3 (m) Study 2 CF333 “DK2” 2007 Yes N/A Late LB 0.5
[126-128] Yang_CF66-2008 Study 2 CF66 “DK2” 2008 No N/A Late LB 0.5
[129-131] SD_CF211-1997 (m) Study 5 CF211 “DK2” 1997 Yes N/A Late LB 1
[132-134] SD_CF211-1997 Study 5 CF211 “DK2” 1997 No N/A Late LB 1
[135-137] SD_CF211-2006 (m) Study 5 CF211 “DK2” 2006 Yes N/A Late LB 1
[138-140] SD_CF211-2006 Study 5 CF211 “DK2” 2006 No N/A Late LB 1
[141-142] Lee_CF30-1992 (m) Study 3 CF30 “DK1” 1973 Yes No Late BB 1
[143-144] Lee_CF30-1992 Study 3 CF30 “DK1” 1973 No No Late BB 1
[145-146] Lee_CF30-2001 (m) Study 3 CF30 “DK1” 2001 Yes No Late BB 1
[147-148] Lee_CF30-2001 Study 3 CF30 “DK1” 2001 No No Late BB 1
[149-150] Lee_CF46-1988 (m) Study 3 CF46 “DK1” 1988 Yes No Late BB 1
[151-152] Lee_CF46-1988 Study 3 CF46 “DK1” 1988 No No Late BB 1
[153-154] Lee_CF46-1997 (m) HYP Study 3 CF46 “DK1” 1997 Yes Yes Late BB 1
[155-156] Lee_CF46-1997 HYP Study 3 CF46 “DK1” 1997 No Yes Late BB 1
[157-158] Lee_CF128-1992 (m) Study 3 CF128 “DK1” 1992 Yes No Late BB 1
[159-160] Lee_CF128-1992 HYP Study 3 CF128 “DK1” 1992 No Yes Late BB 1
[161-162] Lee_CF128-2002 (m) Study 3 CF128 “DK1” 2002 Yes No Late BB 1
[163-164] Lee_CF128-2002 HYP Study 3 CF128 “DK1” 2002 No Yes Late BB 1
[165-167] Hob_1998 Study 4 M “M” 1998 No No Late LB >3
[168-170] Hob_1998 (m) Study 4 M “M” 1998 Yes No Late LB >3
[171-173] Hob_1999 Study 4 M “M” 1999 No No Late LB >3
[174-176] Hob_2001 Study 4 M “M” 2001 No No Late LB >3
[177-179] Hob_1999 HYP Study 4 M “M” 1999 No Yes Late LB >3
[180-182] Hob_2001.1 HYP Study 4 M “M” 2001 No Yes Late LB >3
[183-185] Hob_2001.2 HYP Study 4 M “M” 2001 No Yes Late LB >3
[186-188] Hob_2001.3 HYP Study 4 M “M” 2001 No Yes Late LB >3
  1. 1Adaptation state (early or late).
  2. 2Growth medium for the experiments: Synthetic Cystic Fibrosis Sputum Medium (SCFSM), Luria-Bertani Broth (LB), or Beef Broth (BB).
  3. 3Optical density (OD) at 600 nm during cell harvest.