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Table 1 Burkholderia growth conditions for microarray analysis

From: Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

Time course experiments

ID

Medium

Conditions

OD600

Time pt

Time from t0

Label

1

Nutrient broth

25 C

1

0

 

temp t0

2

Nutrient broth

37 C

0.65

1

20m

temp t1

3

Nutrient broth

37 C

1

2

63m

temp t2

4

Nutrient broth

37 C

1.25

3

78m

temp t3

5

Nutrient broth

37 C

1.5

4

96m

temp t4

6

Nutrient broth

pH 9

0.6

0

 

pH t0

7

Nutrient broth

pH 4

0.7

1

15m

pH t1

8

Nutrient broth

pH 4.5

1

2

15h

pH t2

9

Nutrient broth

pH 4.5

1.2

3

15.6h

pH t3

10

Nutrient broth

pH 5+

1.6

4

15.3h

pH t4

11

Nutrient broth

no salt

0.6

0

 

salt t0

12

Nutrient broth

350mM NaCl

0.7

1

15m

salt t1

13

Nutrient broth

350mM NaCl

1

2

107m

salt t2

14

Nutrient broth

350mM NaCl

1.2

3

147m

salt t3

15

Nutrient broth

350mM NaCl

1.5

4

201m

salt t4

16

M9 succinate

80mM PO4

1

0

 

PO4 t0

17

M9 succinate

40mM PO4

0.6

1

15m

PO4 t1

18

M9 succinate

40mM PO4

0.9

2

97m

PO4 t2

19

M9 succinate

40mM PO4

1.2

3

160m

PO4 t3

20

M9 succinate

20mM PO4

0.6

4

188m

PO4 t4

21

M9 succinate

20mM PO4

0.6

5

363m

PO4 t5

Five replicates for all conditions, except samples at pH 4.5 with 3 replicates.

Single time point experiments

ID

Medium

Temp

Replicates

Description

Label

22

M9 succinate

16

4

temp 16 C

16°C

23

M9 succinate

37

4

temp 37 C

37°C

24

M9 succinate

37

1

70 mM phosphate

PO4

25

M9 succinate

37

1

40 mM phosphate

low PO4

26

M9 succinate

37

1

anaerobic

N

27

M9 succinate

37

1

anaerobic + CO2

N + CO2

28

M9 succinate

37

1

nitrogen-limited

low N

29

M9 succinate

37

1

sulfur-limited

low sulfur

30

M9 succinate

37

1

solid media

solid

31

M9 succinate

37

1

50 mM Mg++

high Mg

32

M9 succinate

37

1

5 uM Mg++

low Mg

33

M9 succinate

37

1

0.07g/L EDTA

EDTA

34

M9 succinate

37

1

0.07g/L EDTA with nutrient-limit

EDTA/limit

35

M9 succinate

37

1

+0.1% phenol

phenol

36

M9 succinate

37

1

+200 ppm Bleach

bleach

37

M9 succinate

37

1

+5% EtOH

ethanol

38

M9 glucose

25

1

M9-glucose

glucose

39

M9 galactose

37

1

M9-galactose

galactose

40

M9 proline

37

1

M9-proline

proline

41

Luria broth

25

4

temp 25 C

25°C

42

Luria broth

37

4

temp 37C

37°C

43

Luria broth

41

4

temp 41 C

42°C

44

Luria broth

37

4

pH 9

pH 9

45

Luria broth

37

4

pH 5

pH 5

46

Luria broth

37

4

80mM Peroxide

H202

47

Luria broth

37

2

0.5M NaCl

NaCl

48

Calf serum

37

4

CS infusion, temp 37 C

37°C

49

Calf serum

37

1

antibiotics

antibiotics

50

Calf serum

37

1

antibiotics + 0.07g/L EDTA

antibiotics + EDTA

51

Calf serum

37

1

aspirin

salicylate

52

Brain heart

37

1

solid media

solid

53

Tryptic soy

37

1

kan mutant

kan mutant

54

Tryptic soy

37

1

wt

wt

  1. The antibiotics treatment consisted of carbenicillin (100 μg/ml), chloramphenicol (30 μg/ml), erythromycin (200 μg/ml, and kanamycin (50 μg/ml). The EDTA concentration of 0.07g/L is standard usage for chelation therapy. The kan mutant (ID53) is a spontaneous B. thailandensis mutant isolated in response to a sublethal exposure to kanamycin.