TABLE 4.
Primers used in this study
| Name | Sequence | Description |
|---|---|---|
| CEA_vec01 | ACTAGTAGCGGCCGCTTAAGCGCTCCCTGCCCGCTGTGG | Amplification integrase φBT1, suffix BioBrick (sites SpeI, NotI and AflII underlined) |
| CEA_vec02 | AATAGGAACTTCCCTGCAGGTGGCGCCGGACGGGGCTTC | Amplification integrase φBT1, site SbfI underlined |
| CEA_vec03 | CCTGCAGGGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCGTCCACGACGCCCGTGATTTTG | Amplification oriT, FRT site added in boldface, site SbfI underlined |
| CEA_vec04 | CTCACCGCGACGTGGTACCCTTTTCCGCTGCATAACCCTG | Amplification oriT, site KpnI underlined |
| CEA_vec05 | GGGTACCACGTCGCGGTGAGTTCAGG | Amplification aac(3)-IV, site KpnI underlined |
| CEA_vec06 | GGATCCGGTTCATGTGCAGCTCCATCAG | Amplification aac(3)-IV, site BamHI underlined |
| CEA_vec07 | GCTGCACATGAACCGGATCCCCTAGCGGAGTGTATACTGG | Amplification of p15A origin of replication, site BamHI underlined |
| CEA_vec08 | GCTAGCAGCGGCCGC ATGCATGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCACAACTTATATCGTATGGGGCTGAC | Amplification of p15A origin of replication, FRT site added in boldface, prefix BioBrick (sites NheI, NotI, and NsiI underlined) |
| CEA_vec09 | TGCATGCGGCCGCTGCTAGCGTTTTTTGATCTCAATCAATAAAG | Amplification amilCP cassette, prefix BioBrick (sites NsiI and NotI underlined) |
| CEA_vec10 | CTTAAGCGGCCGCTACTAGTATATAAACGCAGAAAGGC | Amplification amilCP cassette, suffix BioBrick (sites AflII, NotI, and SpeI underlined) |
| CEA_vec11 | CAGTCCTGCAGGATTCCAGACGTCCCGAAGG | Amplification integrase φC31, site SbfI underlined |
| CEA_vec12 | CAGTCTTAAGCAGGCTTCCCGGGTGTCTC | Amplification integrase φC31, site AflII underlined |
| CEA_vec13 | CAGTCCTGCAGGAACGGTTCTGGCAAATATTC | Amplification integrase pSAM2, site SbfI underlined |
| CEA_vec14 | CAGTCTTAAGGTCAGTCATGCGGGCAAC | Amplification integrase pSAM2, site AflII underlined |
| CEA_vec31 | CAGTCCTGCAGGTCTCGAGCTCGCGAAAG | Amplification integrase VWB, site SbfI underlined |
| CEA_vec32 | CAGTCTTAAGGTCGACCCGTCTGACGCGTGTG | Amplification integrase VWB, site AflII underlined |
| CEA_vec17 | CTATGATCGACTGATGTCATCAGCGGTGGAGTGCAATGTCGTGACACAAGAATCCCTGTTACTTC | Amplification ORF hygromycin resistance for PCR targeting |
| CEA_vec18 | CCTTGCCCCTCCAACGTCATCTCGTTCTCCGCTCATGAGCTCAGGCGCCGGGGGCGGTGT | Amplification ORF hygromycin resistance for PCR targeting |
| CEA_vec19 | CTATGATCGACTGATGTCATCAGCGGTGGAGTGCAATGTCTCGCATGATTGAACAAGATG | Amplification ORF kanamycin resistance for PCR targeting |
| CEA_vec20 | CCTTGCCCCTCCAACGTCATCTCGTTCTCCGCTCATGAGCTCAGAAGAACTCGTCAAGAAG | Amplification ORF kanamycin resistance for PCR targeting |
| CEA_vec21 | CCAACGCACGACCGGCCGCCAGCTGTGCTTCGGTCGACACG | Site-directed mutagenesis of NheI site of φBT1 integrase, base changed underlined (T→C) |
| CEA_vec22 | CGTGTCGACCGAAGCACAGCTGGCGGCCGGTCGTGCGTTGG | Site-directed mutagenesis of NheI site of φBT1 integrase, base changed underlined (A→G) |
| CEA_vec23 | GCTGTGGTGACGAAGGAACTACTCGTTAGCCTAACTAACG | Site-directed mutagenesis of SpeI site of φBT1 integrase, base changed underlined ( A→C) |
| CEA_vec24 | CGTTAGTTAGGCTAACGAGTAGTTCCTTCGTCACCACAGC | Site-directed mutagenesis of SpeI site of φBT1 integrase, base changed underlined (T→G) |
| CEA_vec25 | CTTCCGGCGCACATGGATACCTGCAATCAAGGC | Site-directed mutagenesis of BamHI site of VWB integrase, base changed underlined (C→A) |
| CEA_vec26 | GCCTTGATTGCAGGTATCCATGTGCGCCGGAAG | Site-directed mutagenesis of BamHI site of VWB integrase, base changed underlined (G→T) |
| CEA_vec27 | CATGGAATTCGAGCTCGGTAACCGGGAATCCCCGGGTACGC | Site-directed mutagenesis of BamHI and KpnI sites of integrase pSAM2, bases changed underlined (C→A and G→A) |
| CEA_vec28 | GCGTACCCGGGGATTCCCGGTTACCGAGCTCGAATTCCATG | Site-directed mutagenesis of BamHI and KpnI sites of integrase pSAM2, bases changed underlined (C→T and G→T) |
| CEA_vec_seq_12 | TCTGGCAGCACTTTGAGGAC | Verification primer, in pSAM2 integrase, towards attP |
| CEA_vec_seq_15 | TTCGATCACGTGGGCGAAGC | Verification primer of flp excision |
| CEA_vec_seq16 | TTGCCAAAGGGTTCGTGTAG | Verification primer in oriT, towards attP of φC31 or φBT1 integrases |
| CEA_vec_seq_17 | TCAGGTCACTGTCCTGTTTC | Verification primer in φBT1 integrase, towards attP |
| CEA_vec_seq18 | AATCTTCGCCGACTTCAGC | Verification primer in φC31 integrase, towards attP |
| CEA_vec_seq_19 | GGTTTGAACTTTCCTCCCAATG | Verification primer in amilCP cassette, towards attP of pSAM2 or VWV integrases |
| CEA_vec_seq_20 | GGTGAAGAACCGGGACACC | Verification primer in VWB integrase, towards attP |
| CEA042 | GTGGTGTCGCGGAACAGACG | Verification primer in M145 and TK23, upstream of φBT1 attB site |
| CEA043 | TCCGCGACGATCCACGAC | Verification primer in M145 and TK23, downstream of φBT1 attB site |
| CEA044 | GCGTGGCGTGGACCATC | Verification primer in M145 and TK23, upstream of φC31 attB site |
| CEA045 | AATGACCTCCGGGCTTTCG | Verification primer in M145 and TK23, downstream of φC31 attB site |
| CEA046 | ACCGGCACCGCATGGCAG | Verification primer in M145 and TK23, upstream of pSAM2 attB site |
| CEA047 | ACGGCGCGTGCGGCATC | Verification primer in M145 and TK23, downstream of pSAM2 attB site |
| CEA048 | GAAAGACGGCCGACCACC | Verification primer in M145 and TK23, upstream of VWB attB site |
| CEA049 | TGCCCGCCCTCTGCATC | Verification primer in M145, downstream of VWB attB site |
| CEA050 | CTGTATGCCGCCGTCCCG | Verification primer in TK23, downstream of VWB attB site |
| CEA051 | GGTGGTGTCCCGGACCAG | Verification primer in J1074, upstream of φBT1 attB site |
| CEA052 | CCGCGACGATCCAGGACC | Verification primer in J1074, downstream of φBT1 attB site |
| CEA053 | GGCGTGGATCATGGTGATCG | Verification primer in J1074, upstream of φC31 attB site |
| CEA054 | GGTTGCGGGTGGCAAGTAG | Verification primer in J1074, downstream of φC31 attB site |
| CEA055 | CGGCCAGCTCTGCATCCC | Verification primer in J1074, upstream of pSAM2 attB site |
| CEA056 | CGGATTGTTTGCCGCCTTC | Verification primer in J1074, downstream of pSAM2 attB site |
| CEA057 | GCATGCACGGCGACCTG | Verification primer in J1074, upstream of VWB attB site |
| CEA058 | GTGACCCTGCCGGGATGG | Verification primer in J1074, upstream of VWB attB site |
| CEA_seq24 | ACCATCGCCCACGCATAAC | Verification of the loss of pUWLHFLP |
| Thio_fwd | TTGGACACCATCGCAAATC | Verification of the loss of pUWLHFLP |
| CEA036 | AAAATGCATGCGGCCGCTGCTAGCGGTGAGGCGCCACCCATCG | Amplification albonoursin cluster (sites NsiI, NotI, and NheI underlined) |
| CEA038 | AAACTTAAGGCGGCCGCTACTAGTCCGCACCATGAGCAAGTGTC | Amplification albonoursin cluster (sites AflII, NotI, and SpeI underlined) |
| F_pref_rpslp_TP | ATGCATGCGGCCGCTTCTAGAGACCGGGTCCGCGATCGGCGG | Amplification rpsl(TP)p (sites NsiI, NotI and XbaI underlined) |
| R_suff_rpslp_TP | CTTAAGGCGGCCGCTACTAGTGCTCCCTTCTCAGAAGCGCAGG | Amplification rpsl(TP)p (sites AflII, NotI and SpeI underlined) |
| onCAS001bis | GCTGCTAGCTGTTCACATTCGAACCGTCTCTG | Amplification SP22 promoter forward (truncated NotI and NheI underlined) |
| onCAS002 | ATGGACACTCCTTACTTAGAC | Amplification SP22 promoter reverse |
| onCAS003 | GTATAGGAACTTCATGCATGCGGCCGCTGCTAGCTGTTCACATTCGAACCG | Bridging oligonucleotide between plasmid pOSV812 and SP22 promoter |
| Bridge4 | ACGGTTTACAAGCATAACTAGTAGCGGCCGCTTAAGGTCGACCCGTCTG | Bridging oligonucleotide between T4 terminator and pOSV812 |
| onCAS007 | TGATCCGGTGGATGACCTTTTG | Amplification T4 terminator forward |
| onCAS008bis | GCTACTAGTTATGCTTGTAAACCGTTTTG | Amplification T4 terminator reverse (truncated NotI and SpeI underlined) |
| onCAS031 | ATGGCCACCGAGTCCGCCACC | Amplification cgc22 forward |
| onCAS032 | CTACCCGCCGTCGCCGTCGC | Amplification cgc22 reverse |
| onCAS033 | GAATACGACAGTCTAAGTAAGGAGTGTCCATATGGCCACCGAGTCCGCC | Bridging oligonucleotide between SP22 promoter and cgc22 |
| onCAS034 | GACGGCGACGGCGGGTAGTGATCCGGTGGATGACCTTTTGAATGAC | Bridging oligonucleotide between cgc22 and T4 terminator |
| on-ori | ATTTCAGTGCAATTTATCTCTTC | Universal sequencing primer in p15A origin for verification of the insert |