Table 1. Synthetic oligonucleotides used in the study.

Name	Primer sequence	Position
MUC4 promoter sequencing primers
MUC4-S1L	AGGCAGAACAGAGCTCAAATTC	−3647 to −3626
MUC4-S1R	ACAAAATGAGTGGCTTCTCTAGTTC	−2970 to −2946
MUC4-S2L	ACTTACACCTGACTTCAGACTCCTG	−3047 to −3023
MUC4-S2R	TTCCTCGTTCACCTGTAAAATG	−2,410 to −2389
MUC4-S3L	AACCAGGTGTCGTAACAACAAG	−2523 to −2504
MUC4-S3R	ACCATCTCAGCTCACTGCAAG	−1846 to −1826
MUC4-S4L	AAGAGCTGACAGAAAAATGACCAC	−2,092 to −2,069
MUC4-S4R	TGTAGCTCTCTGCAAAGGAAAAC	−1236 to −1214
MUC4-S5L	CCATGAACAGACTTTCAGCTTCTAG	−1521 to −1497
MUC4-S5R	CCAGATGGTGGACTTCTTCTTTC	−958 to −936
MUC4-S6L	CCTACCGAGGTTTTGCCTTC	−1063 to −1044
MUC4-S6R	CTAATCACCCTTTTCTCTCCTCAG	−194 to −171
MUC4-S7F	CATACAGTGCATTTCTGTTCCTG	−557 to −535
MUC4-S7R	ATCACTTACCTGGGACCACATG	+70 to +91
10mer-tagged or T7-tagged primers a
MUC4-1L	aggaagagagTGTGTGGTTTAGAAGGTTGTAATTG	−3611 to −3587
MUC4-1R	cagtaatacgactcactatagggagaaggctACCCAAATAAAAATCCCTAATTTTT	−3233 to −3208
MUC4-2L	aggaagagagTGGGAGAATTTTATGATTTTATTTTTGTT	−3134 to −3106
MUC4-2R	cagtaatacgactcactatagggagaaggctATTTCCAAACCCAAATCTTTCCTAC	−2671 to −2647
MUC4-3L	aggaagagagGTAGGAAAGATTTGGGTTTGGAAAT	−2671 to −2647
MUC4-3R	cagtaatacgactcactatagggagaaggctAACATCCAAATAAAACCAAACTAAAC	−2204 to −2179
MUC4-4L	aggaagagagTGTGTGTTTTTGGTTTTTTTGGTAT	−2274 to −2250
MUC4-4R	cagtaatacgactcactatagggagaaggctACACCATCTCAACTCACTACAAACTC	−1849 to −1824
MUC4-5L	aggaagagagTAGTTTTTTGTTTTGGAAAGAAGAAGTTTA	−973 to −944
MUC4-5R	cagtaatacgactcactatagggagaaggctAACAAACCCCAAAAAATTAAAAAAC	−512 to −488
MUC4-6L	aggaagagagGGTTTGTTATGTGTTTGGGATTTG	−793 to −770
MUC4-6R	cagtaatacgactcactatagggagaaggctAAAATAAATAAACCACCCTCCTAAC	−344 to −320
MUC4-7Lb	aggaagagagTAGGGATATTTAGGGGATTTTTTTT	+18 to +42
MUC4-7Rb	cagtaatacgactcactatagggagaaggctTTCCCAACAACCCAAAACTCTAATA	−415 to −391
MSP primers
MSP-ULc	GGTGATTAGTGTGGGGTTTTG	−179 to −159
MSP-UR	CCAAACCAAATACATTTCTCCAA	−122 to −100
MSP-MLd	GGTGATTAGCGTGGGGTTTC	−179 to −160
MSP-MR	CGAACCAAATACGTTTCTCCG	−121 to −101

^aL=(aggaagagag) + (gene-specific sequence), R=(cagtaatacgactcactatagggagaaggct) + (gene-specific sequence).

^bMUC4-7L and MUC4-7R primers were designed for the antisense strand because PCR amplification was not obtained in the forward direction.

^cU indicates the primer for unmethylated alleles.

^dM indicates the primer for methylated alleles.