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Table 1 Summary of candidate genes selected for validation as reference genes

From: Validation of miRNA genes suitable as reference genes in qPCR analyses of miRNA gene expression in Atlantic salmon (Salmo salar)

miRNA gene1

Source2

Similar paralog3

Clustered genes4

CV Deep seq.5

qPCR validation6

ssa-miR-103-3p

Liang, P&L, Bar

no

not clustered

99,3

not included

ssa-miR-106a-5p

P&L

yes

25,93

-

-

ssa-miR-106b-5p

Liang

yes

25,93

-

-

ssa-miR-107-3p

Bar

no

not clustered

85,5

yes

ssa-miR139-5p

Bar

no

not clustered

138,5

not included

ssa-miR-140-3p

Liang

no

not clustered

172,6 (71,7)

yes

ssa-miR-148a-3p

Bar

yes

not clustered

-

-

ssa-miR-152-3p

Liang

no

not clustered

122,4

not included

ssa-miR-15b-5p

Liang

yes

16

-

-

ssa-miR-16a-5p

Liang, P&L, Appl

yes

15

-

-

ssa-miR-17-5p

P&L

no

18,19,20,92

77

yes

ssa-miR-183-5p

Bar

no

96,182

286,3

yes

ssa-miR-18a-5p

Bar

yes

17,19,20,92

-

-

ssa-miR-214-3p

Bar

no

not clustered

82,6

failed

ssa-miR-23a-3p

Bar

yes

24,27

-

-

ssa-miR-23b-3p

Bar

yes

24,27

-

-

ssa-miR-24a-3p P&L

yes

23,27

-

-

 

ssa-miR-25-3p P&L

no

93,106

53,6

yes

 

ssa-miR-26a-5p

Bar

yes

181

-

-

ssa-miR-26b-5p

Bar, Appl

yes

181

-

-

ssa-miR-29a-3p

Liang

yes

29b

-

-

ssa-miR-29b-3p

Liang

yes

29a

-

-

ssa-miR-30b-5p

Bar

yes

30e

-

-

ssa-miR-30d-5p

Bar

yes

30a

-

-

ssa-miR-30e-5p

Liang

yes

30d

-

-

ssa-miR-301a-3p

Genov

yes

not

clustered

-

ssa-miR-92a-3p

Liang, Bar, Appl

yes

17,18,19,20

-

-

ssa-miR-93a-5p

Liang, P&L, Bar

no

25,106

73,5

yes

ssa-miR-99-5p P&L

no

let-7c,7b

127,6

not

included

ssa-let-7a-5p P&L

yes

7f,100

-

-

 

ssa-miR-455-5p

deep-seq

no

not clustered

128 (48)

yes

ssa-miR-210-5p

deep-seq

no

not clustered

184,9 (89,9)

yes

  1. 1All salmon miRNA genes selected for validation as reference genes annotated as in Andreassen et al. [13].
  2. 2The source for selecting each miRNA gene for validation is given in this column. References are Liang [30], P&L (Peltier and Latham) [26], Bar (Bargaje et al.) [31], Genov (Genovesi et al. [29]), Appl; Applied biosystems TaqMan controls, Deep-seq; these were suggested as reference genes by their high stability in deep sequence data.
  3. 3miRNA genes that has highly similar paralogous mature miRNAs in Atlantic salmon.
  4. 4If located in a miRNA gene cluster the identity of the other miRNA genes in the cluster is gives as their gene number.
  5. 5The covariation of all candidate miRNA genes that were selected for stability testing in deep-sequencing data. Covariation if removing one deep sequencing sample in three of the miRNAs (see Additional file 1) in parenthesis.
  6. 6Denoted yes means they were selected for experimental validation by qPCR.