Nature - USA (2020-10-15)

Up in 25C plate vs liquid

Up in 25C plate vs 15C plate

Up in 25C plate vs both

25C upregulated

PA14 small RNAs

b

ErsA

P2^4

Sr3^2

RsmZ

P1 6

P1

1

0 kb

500 kb

1000 kb

1500 kb

2000 kb

2500

kb

4000 kb

4500 kb

5000 kb

5500

kb

6000 kb

PA14 genome

3000 kb

3500 kb

a

−10

−5

05

−10

(^01020)
PC1: 27% variance
PC2: 17% va
riance
10
Liquid
grown
PA14
PA14
lawn
(25°C)
PA14
lawn
(15°C)
c d
upregulated
sRNA
25C vs liquid
(16)
upregulated
sRNA
25C vs 15C
(12)
P1 1
P1 6
P2 4
Sr32
RsmZ
ErsA
Extended Data Fig. 5 | RNA sequencing of sRNAs from PA14. a, sRNA training
protocol using RNA isolated from PA14 cultures grown at 25 °C or 15 °C on
plates, or in liquid culture. b, Principal component analysis of PA14 sRNA
sequencing. c, Upregulated sRNAs in 25-°C grown PA14 compared to
15 °C-grown and liquid-grown PA14 sRNAs. The outermost grey circle
represents the PA14 genome, with previously identified sRNAs that were
upregulated (DESeq2, adjusted P ≤ 0.05) in the 25-°C plate condition relative to
15-°C plate grown PA14 (pink) or liquid-grown PA14 (green) are indicated.
Overlapping sRNAs upregulated in the 25-°C plate condition relative to both
other conditions are noted (blue dots). sRNAs annotated with white lines.
d, Venn diagram showing the number of PA14 sRNAs upregulated at 25-°C
growth conditions compared to liquid growth (blue circle) or 15-°C growth
(red circle). The six shared upregulated sRNAs are shown.