. 2015 Mar 18;10(3):e0118424. doi: 10.1371/journal.pone.0118424

Table 2. Oligonucleotides used for the detection and discrimination of exogenous and endogenous sequences and oligonucleotides used for real-time qPCR.

Fragment	Primer name (orientation), primer sequences (5ˈ → 3ˈ)	PCR product (bp)
Endogenous factors
*SOX2*	G0086 (fwd): TCTTCCTCGCACTCCAGGGC	228
*SOX2*	G0030 (rev): CCGCTCGAGAATGCCTCCCCCGTCCAGTTCG	228
*OCT4*	G0022 (fwd): GATCGGATCCTTGGGGCGCCTTCCTTC	510
*OCT4*	G0035 (rev): CAGGGTGATCCTCTTCTGCTTC	510
*KLF4*	G0091 (fwd): GGAAGACGATCTTGGCCCCG	323
*KLF4*	G0021 (rev): GTACTCTAGACAGTGTGGGTCATATCCACTG	323
*c-MYC*	G0079 (fwd): ATAAGAATGCGGCCGCACTGGATTTTTTTCGGGCAGTGG	456
*c-MYC*	G00142 (rev): CCTGGATGATGATGTTTTTGATG	456
*LIN28*	G0305 (fwd): GACGAGCTGTACAAGGGGAGTGAGAGGCGGCCAAAGGGG	334
*LIN28*	G0025 (rev): GACTCTCGAGATAGCCAAAGAATAGCCCC	334
*NANOG*	G0018 (fwd): GATCAAGCTTCCTTTTCCCCAATAATAACATG	754
*NANOG*	G0075 (rev): TTATAGAAGGGACTGCTCCAGG	754
Reprogramming cassette
*SO (SOX2-OCT4)*	G0086 (fwd): TCTTCCTCGCACTCCAGGGC	735
*SO (SOX2-OCT4)*	G0035 (rev): CAGGGTGATCCTCTTCTGCTTC	735
*IC (IRES-Cerulean)*	G0095 (fwd): AGCGACCCTTTGCAGGCAGC	1073
*IC (IRES-Cerulean)*	G0039 (rev): GAAGATCTACTTGTACAGCTCGTCCATG	1073
*PCAG-SOX2*	G0244 (fwd): GGGGACGGCTGCCTTCGG	190
*PCAG-SOX2*	G0378 (rev): GCTCGGTACCAAGCTTAAG	190
*PCAG-SOX2*	G0244 (fwd): GGGGACGGCTGCCTTCGG	361
*PCAG-SOX2*	G0395 (rev): CGGTCGGGGCTGTTCTTCTG	361
*NANOG-IRES*	G0069 (fwd): GGTTCCAGAACCAGAGAATGAAATC	576
*NANOG-IRES*	G0098 (rev): CACCGGCCTTATTCCAAGCG	576
*Cerulean*	G0618 (fwd): ACGTAAACGGCCACAAGTTCAGC	211
*Cerulean*	G0619 (rev): CCTTCGGGCATGGCGGACTTG	211
Control fragments
*mmSox2*	G0656 (fwd): GGACATGATCAGCATGTACCTCC	221
*mmSox2*	G0657 (rev): TCTCCTCTTTTTGCACCCCTCC	221
*β-ACTIN*	G0336 (fwd): GACGACATGGAGAAGATCTGG	562
*β-ACTIN*	G0337 (rev): GGAAAGAAGGCTGGAAGAGTG	562
Real-time qPCR
*18S rRNA*	G0871 (fwd): ATTAAGGGTGTGGGCCGAAG	81
*18S rRNA*	G0872 (rev): GAGTTCTCCTGCCCTCTTGG	81
*OCT4_endo (isoform A and B)*	G0963 (fwd): GCCAGGGCTTTTAGGATTAAGTT	68
*OCT4_endo (isoform A and B)*	G0964 (rev): TGCCCTCACCCTTTGTGTTC	68
*OCT4A_endo+exo*	G0877 (fwd): CCCCTGGTGCCGTGAAG	82
*OCT4A_endo+exo*	G0878 (rev): TTCTGCAGAGCTTTGATGTCTTG	82
*NANOG*	G0965 (fwd): ATGCCACCTGAAGATGTGTGAA	69
*NANOG*	G0966 (rev): TCAGCCAGTGCTCAGAGTGAA	69
*Transposon*	G0961 (fwd): AGCCAACATACTTTCGGGAGGA	135
*Transposon*	G0962 (rev): TACTCATTGGGCCAGGATTCTC	135
*SOX2*	G0969 (fwd): TTGTTCAAAAAAGTATCAGGAGTTGTC	97
*SOX2*	G0970 (rev): CTCTCCGTCCCCGTCTTAAAG	97
*LIN28*	G0682 (fwd): GCACAGGGAAAGCCAACATAC	126
*LIN28*	G0683 (rev): CGAAACTTCCTGATAGCCAAAGA	126