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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.