Table 3

Reliability examination of the randomly selected 30 feeding Ahringer C. elegans RNAi bacterial strains with different scores

Information provided by the manufacturer

Information based on direct sequencing analysis

Seq. No.

Reliability score

GenePairs name

GeneService location

Predictable by MFEprimer

GenePairs name

GeneService location

Predictable by MFEprimer

Reliability examination manually

Comment


1

100

F18H3.3

X-6I10

F18H3.3

X-6I10

2

100

F22E12.4

V-7A24

F22E12.4

V-7A24

3

100

T07D1.4

X-1J16

T07D1.4

X-1J16

4

100

K09G1.4

V-6P21

K09G1.4

V-6P21

5

100

T26G10.1

III-5C07

T26G10.1

III-5C07

6

100

W01C9.5

II-6A04

W01C9.5

II-6A04

7

49

F36H12.3

IV-2B04

F36H12.17

IV-2D04

×

Remapped. Probably sample loading error: position of the strain was shifted vertically for two rows in same column of the same plate.

8

48

C17C3.13

II-4D02

C17C3.13

II-4D02

9

48

M142.1

III-5F06

F54F12.2

III-6D13

Remapped. Nonspecific amplicon and may be prevented by MFEprimer evaluation on the primer set at first.

10

46

T08D2.2

V-13E02

W07B8.1

NA (not in the library)

Remapped. Nonspecific amplicon and may be prevented by MFEprimer evaluation on the primer set at first.

11

44

T17A3.3

III-1E13

NA

NA

×

×

Empty vector construction based on direct sequencing

12

42

F58B4.1

V-7B19

F58B4.1

V-7B19

13

36

F48G7.5

V-1G12

F48G7.5

V-1G12

14

32

F32B5.4

I-1I14

C45E1.1

I-1M14

×

Remapped. Probably sample loading error: position of the strain was shifted vertically for four rows in same column of the same plate.

15

30

K11H12.1

IV-1A12

K11H12.1

IV-1A12

16

28

C03H5.5

II-1O03

Y48G8AL.11

NA (not in the library)

Remapped. Nonspecific amplicon and may be prevented by MFEprimer evaluation on the primer set at first.

17

27

C32E8.3

I-1H21

C32E8.3

I-1H21

18

26

F10G8.2

I-5C13

F10G8.2

I-5C13

19

24

C14B1.10

III-1J10

NA

NA

×

Nonspecific amplicon (Intergenic region [438973..440037] in chromosome I) and may be prevented by MFEprimer evaluation on the primer set at first.

20

23

F59H6.8

II-2E10

F59H6.8

II-2E10

21

22

R09A1.2

V-1F13

NA

NA

×

Nonspecific amplicon (Intergenic region [3064499..3065944] in chromosome V) and may be prevented by MFEprimer evaluation on the primer set at first.

22

22

B0554.1

V-1K09

Y39D8A.1

V-1K07

×

Remapped. Probably sample loading error by the manufacture: position of the strain was shifted horizontally for two columns in same row of the same plate.

23

20

C45G7.5

IV-1N13

C45G7.5

IV-1N13

24

14

W02G9.1

V-2M18

W02G9.1

V-2M18

25

4

C49A1.1

I-7I17

Y48G8AL.13

NA (not in the library)

Remapped. Nonspecific amplicon and may be prevented by MFEprimer evaluation on the primer set at first.

26

0

Y110A2A_4093.a

II-9H01

×

K02F6.9

NA (not in the library)

Retired gene name and remapped to the new gene.

27

0

C38H2.2

III-5F21

×

NA

NA

×

×

Nonspecific amplicon (Located in chromosome X according to the BLAST similarity search) and may be prevented by MFEprimer evaluation on the primer set at first.

28

0

Y119D3_462.c

III-7A23

×

Y119D3A.2

NA (not in the library)

Retired gene name and remapped to the new gene.

29

0

Y55B1B_119.g

III-7G04

×

Multiple targets predicted

NA

×

Retired gene name and remapped to multiple new genes.

30

0

Y67D8A_349.a

IV-8B22

×

NA

NA

×

×

Retired


Note: NA represents for "not available".

Qu et al. BMC Genomics 2011 12:170   doi:10.1186/1471-2164-12-170

Open Data