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Table 2 Quantitative PCR validation of the CGH experiments

From: Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

Gene/region

forward primer

reverse primer

amplification efficiency (%)

reference strain

experimental strain

ratio (mean ± SD, n = 3)

ratio for region (CGH)

R26S (ref. gene)

GCTAGGCTTGCGTTTGTGTG

GGCGAGACAGAAAGATTCCG

108

strain 1

strain 2/3

-

-

Dynein (ref. gene)

GGAACAAAGCATGGTGACAACA

CGCGTGCCTATCCAAGCT

97

strain 1

strain 2/3

-

-

Sctg_16

GCGTGCGTGCTTGGAAGG

TTCGGCTGCTGAGAGTGGAG

96

strain 1

strain 3

0.9 ± 0.04

0.5

Sctg_16

CAACCGCTCTCCACCATTCAG

GACGCCTTCACAGTATCACACC

96

strain 1

strain 3

0.7 ± 0.02

 

Sctg_16

AACGATAGAGCGAGACGAGAGAG

GGAAGCAGATGGACACGAGTAAC

93

strain 1

strain 3

0.8 ± 0.03

 

Sctg_68

CTCCTATCGCCCTGTGGTCTC

ACTGCCTCTATGGTCCGTCTTG

100

strain 1

strain 2

1.0 ± 0.1

0.4

Sctg_68

GTGAGAGAAACAACAGAGCAATACAG

ATGGAACCGCAGACAACAAGC

102

strain 1

strain 2

0.6 ± 0.2

 

Sctg_68

TCCGACCTGACGAGCATTGG

CAGTGTGCGGTGCGAACG

103

strain 1

strain 2

n/a*

 

Sctg_68

AAACACCTCCCAACCAACCAATC

AACGCAACGAGCAACCTTCC

100

strain 1

strain 2

n/a*

 

EsV-1

TAAGTTGATATTAGTGACAGTAGCAGGAG

GCCACGGAGGACGGAGATAC

101

strain 1

strain 2

n/a*

0.5

EsV-1

ACCACGATGCCTGTCTCCTTAC

TCCTCAGCCGCCAGAATACG

95

strain 1

strain 2

n/a*

 

EsV-1

CTCCTCCGTAACCGTTGACATTG

CCGACCAGTAAACCCGTAAACC

101

strain 1

strain 2

n/a*

 
  1. * no amplification in experimental strain, or difference > 10 cycles
  2. Primers and validation results for each tested genomic region (EsV-1 = region on Sctg_52 containing the E. siliculous virus 1 genes, ref. gene = reference gene). The amplification efficiency was calculated from the standard curve for strain 1.