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Table 13 ∆∆Cq calculation performed on ten uni-gene sequences that were selected for validation. The six sequences were the unknown sequences (two upregulated and four downregulated), one was the FoxP3 gene and three sequences that had BLAST hits homologous to other species. Uni-gene 1 _CL2788Contig1 and 1_CL2766Contig1 were not reported as those uni-genes were discarded halfway through the qRT-PCR analysis. The average of GAPDH Cq is used to normalise the target gene expression *Exprs - Expression

From: Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection

Days P.I.

Cq of GAPDH (REF)

Uni-gene Name

Cq of Gene (TAR)

∆Cq

∆Cq Exps

Average ∆Cq Exps

∆Cq Exprs SD

∆∆Cq

∆∆Cq SD

KD%

Day 3

22.54

1_CL1597Contig1

31

8.04

0.003

0.002

0.001453

0.171016

0.090154

82%

22.86

32.13

9.17

0.001

22.91

1_CL2708Contig1

30.03

7.07

0.007

0.006

0.001648

0.196888

0.051999

80%

22.95

30.58

7.62

0.005

23.08

FoxP3(1_CL2412Contig1

NO EXPRESSION

23.40

23.11

1_CL41Contig6

31.40

8.44

0.002

1,973,293.77

2,790,659

7.586422

10.72882

-VE VALUE

22.82

1.04

− 21.91

3,946,587.54

22.88

1_CL2624Contig1

37.25

14.29

0.00

1,493,899.42

2,112,693

9,999,717

14,141,736

-VE VALUE

23.24

1.44

−21.51

2,987,798.85

23.29

1_CL1576Contig

37.23

14.27

0.00

0.000

8.55E-05

0.000291

0.000224

99%

23.51

35.46

12.51

0.00

22.99

1_CL1679Contig1

NO EXPRESSION

22.84

23.12

1_CL2484Contig1

36.15

13.19

0.00

0.000

7.3E-05

0.005133

0.002365

99%

22.44

35.17

12.21

0.00

22.56

22.64

AVERAGE (REF)

22.95