Table 2 Summary of restriction enzyme cutting abnormality (RECA)

A

A1: cDNA is inversely inserted

5′: N,3TNS-1,V,3TSS-2

3′: 5TNS-2,V,5TSS-1,N

5′: a cDNA non-sense strand

3′: a cDNA sense strand

FLD1_38_A06.g1_A029 (Fig. S2 A)

RTDR3_19_H01.b1_A022 (Fig. S2 B)

A2: cDNA is inserted without inversion

5′: 5TSS,N,V,3TSS-2

3′: 5TNS-2,V,N,3TNS

5′: a cDNA sense strand

3′: a cDNA non-sense strand

RTDR1_20_F07.g1_A015 (Fig. S2 C)

RTMNUT1_27_H12.g1_A029 (Fig. S2 D)

STRS1_37_H01.b1_A034 (Fig. S2 E)

A3: Adapter/linker fragments are inserted

5′:5TSS,3TNS-1,V,3TSS-2

3′:5TNS-2,V,5TSS-1,3TNS

No cDNA

NXRV076_A06_F (Fig. S2 F)

B

B1: cDNA is inversely inserted

5′: 5TSS-2,V,5TNS-1,N

3′: N,3TSS-1,V,3TNS-2

5′: a cDNA non-sense strand

3′: a cDNA sense strand

NXRV_013_E07_F (Fig. S2 G)

RTDS1_2_A09.b1_A015 (Fig. S2 H)

B2: cDNA is inserted (non-inversely)

5′: 5TSS-2,V,N,3TSS

3′: 5TNS,N,V,3TNS-2

5′: a cDNA sense strand

3′: a cDNA non-sense strand

RTFEPL1_26_F12.g1_A029 (Fig. S2 I)

RTFEPL1_26_F12.b1_A029 (Fig. S2 J)

C

Neither of the two enzyme sites is cut off.

5′: 5TSS-2,V,3TSS-2

3′: 5TNS-2,V,3TNS-2

No cDNA

NXCI_011_D03_F (Fig. S2 K)

NXCI_029_D07_F (Fig. S2 L)

D

Both the two enzyme sites are cut off, but the vector fragment that should be removed still remains.

5′: N,3TNS-1,V,5TNS-1,N

3′: N,3TSS-1,V,5TSS-1,N

5′: two cDNA non-sense strands

3′: two cDNA sense strands

RTCNT1_24_B05.g1_A029 (Fig. S2 M)

E

XhoI cuts off at wrong site from the vector.

5′: N,V,3TSS-2

3′: 5TNS-2,V,N

5′: a cDNA sense strand

3′: a cDNA non-sense strand

COLD1_26_G12.b1_A029 (Fig. S2 N)

F

EcoRI cuts off at wrong site from the vector.

5′: V,N

3′: N,V

5′: a cDNA sense strand

3′: a cDNA non-sense strand

RTCA1_14_E09.g1_A029 (Fig. S2 O)