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Table 1 Genes whose expression was validated using RT-qPCR with purified RNA from H. parasuis Nagasaki recovered after 2 h incubation in lung explants (ex vivo), 2 h after intratracheal infection (in vivo) and lung samples from a time-course intranasal infection (1 dpi, 2 dpi and 3 dpi)

From: Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection

Locus tag

Gene type

RT-qPCR 1

á…Ÿ

RNAseq

ex vivo

in vivo

1 dpi

2 dpi

3 dpi

Product

ex vivo

in vivo

logFC

logFC

HPNK_10441

Virulence factor

ND2

4.8

4.2

3.7

4.6

ABC transporter, permease protein

4.2

4.0

HPNK_06205

Virulence factor

ND

4.9

4.6

2.9

4.9

Hypothetical protein

2.1

6.0

HPNK_09829

Virulence factor

ND

3.6

4.1

1.4

3.3

Hypothetical protein

5.2

2.8

HPNK_10446

Virulence factor

ND

3.3

3.5

2.4

3.1

Hypothetical protein

3.1

5.5

HPNK_11461

Virulence factor

ND

5.2

2.1

2.2

2.9

Hypothetical protein

1.8

3.8

HPNK_06565

Virulence factor

ND

5.4

HCT 3

HCT

3.7

Na+/H+ antiporter NhaC

2.3

3.3

HPNK_01698

Virulence factor

ND

4.1

3.8

3.2

3.0

VtaA2

1.6

3.1

HPNK_03728

Key pathway

2.3

5.0

ND

ND

ND

6-pyruvoyl tetrahydrobiopterin synthase

2.6

1.7

HPNK_08953

Key pathway

4.3

2.4

ND

ND

ND

ABC transporter inner membrane subunit

7.3

3.4

HPNK_06845

Key pathway

3.9

5.3

ND

ND

ND

Anthranilate synthase component II

9.1

1.8

HPNK_01064

Key pathway

1.3

5.9

ND

ND

ND

Heme exporter protein D

1.2

2.0

HPNK_10256

Key pathway

−2.8

0.6

ND

ND

ND

PTS mannose-specific transporter subunit

−3.2

−1.9

HPNK_05784

Key pathway

−4.2

−0.6

ND

ND

ND

Type II citrate synthase

−4.7

−3.4

HPNK_02274

Reference

ND

-

-

-

-

BirA repressor

−0.1

−0.1

HPNK_07913

Reference

ND

-

-

-

-

MurE ligase

−0.1

0.1

HPNK_00732

Reference

-

ND

ND

ND

ND

50S ribosomal protein L5

−0.5

−1.7

HPNK_07703

Reference

-

ND

ND

ND

ND

Translocation protein TolB

−0.2

−0.4

HPNK_09689

Reference

-

ND

ND

ND

ND

50S ribosomal protein L2

0.7

−0.6

HPNK_01728

Reference

-

ND

ND

ND

ND

pyruvate dehydrogenase subunit E1

0.0

−1.7

  1. 1log2 fold changes; 2Not determined; 3the gene was amplified but the high CT values obtained were not sufficient to calculate differential expression.