Table 3 Summary of differential expression comparisons performed in CLC Genomics Workbench. Expression values were normalised and significant difference ascertained by Baggerley's test, with FDR-corrected p value cutoff at 0.1%. Contigs were selected for up-regulation in males over females, and 3-5h embryos over 2-3h embryos using normalised fold-change.

Male/Female comparisons

A

Late only (3-5h)

1,2 vs 3,4

2

0

0

B

Late only (3-5h), excl. BJ1

2 vs 3,4

21

9

†mean normalised RPKM of female samples <5

5

C

Early only (2-3h)

5,6 vs 7,8

73

4

†mean normalised RPKM of female samples <5

0

D

Early only (2-3h), excl. BJ5

6 vs 7,8

142

46

†mean normalised RPKM of female samples <5

4

E

Both (3-5h and 2-3h)

1,2,5,6 vs 3,4,7,8

0

0

F

Both (3-5h and 2-3h) excl. BJ1 and BJ5

2,6 vs 3,4,7,8

0

0

G

Both (3-5h and 2-3h) excl. BJ1

2,5,6 vs 3,4,7,8

0

0

Time comparisons

H

Both (Male and female)

1,2,3,4 vs 5,6,7,8

283

86

I

Both (Male and female) excl. BJ1 and BJ5

2,3,4 vs 6,7,8

2313

1213

#mean normalised RPKM of 2-3h samples <50

1051*

J

Both (Male and female) excl. BJ1

2,3,4 vs 5,6,7,8

1846

1128

#mean normalised RPKM of 2-3h samples <50

1019

K

Male only

1,2 vs 5,6

14

2

L

Male only excl. BJ1 and BJ5

2 vs 6

1321

827

#mean normalised RPKM of 2-3h samples <50

673*

M

Male only excl. BJ2 and BJ6

1 vs 5

183

66

N

Female only

3,4 vs 7,8

1980

862*

Intersections

341

(I ∩ L) - (I ∩ L ∩ N)

105