Table 2 Primer sequences for PSQ
From: Diagnostic markers of urothelial cancer based on DNA methylation analysis
Gene | Annotation | Forward | Reverse | Sequencing | Sequence analyzed | Amplicon location relative to transcription start site |
|---|---|---|---|---|---|---|
SOX1 | Sex determining region Y box1 | GGTATTTGGGATTAGTATATGTTTAG | CTATCTCCTTCCTCCTAC | TTAGTATATGTTTAG | CGTACGCGGCGCGTCG | -462~ -351 |
TJP2 | Tight junction protein 2 | GGTTTTTAGATAGGATTTAAAATTTTGAG | CAAAACCTCACACAAACAACTTC | AGGTTTTTTTAGTT | CGATTTTTCG | -492~ -409 |
MYOD1 | Myogenic differentiation 1 | GTGGGTATTTAGATTGTTAGTA | ACAATAACTCCATATCCTAAC | GAAGTTAGGAT | CGTGTCGCGTTATCG | +96~ +233 |
HOXA9_1 | Homeo box A9 | TTGTTTAATTTTATGTGAGGGGTTT | CAAATCTAACCTTATCTCTATACTCTCCC | TGATATAAAATAGTT | CGTTTAAG | -397~ -243 |
HOXA9_2 | Homeo box A9 | ATGAAATTTGTAGTTTTATAATTTT | ATTACCCAAAACCCCAATAATAAC | GTTTTATAATTTT | CGTGGGTCGGGTCGGGCGG | +10~ +100 |
GALR1 | Galanin receptor 1 | ATTAATGGA TGAGGAGGTT | ATACCAAAAA CTTCTCTACT AC | GTGATTTTTA AGGGG | CGCGGATTTT AGTCGAGTTG | -194~ +110 |
IPF1 | Insulin promoter factor 1 | GTAGTTTTAA GAGGAAGG | AAAAATTAAA ACCCATTTAA CCAA | GTAGTTTTAA GAGGAAGGT | CGCGTTTTTTTTTTTCGTTG | -786~ -702 |
TAL1 | T-cell acute lymphocytic leukemia 1 | GTAAATAGAA GGAGGTTTT | ACACTACTTT CAAAAATATA AC | AGAA GGAGGTTTT | CGTAG TTAATTTAAG ATTTCG | -613~ -470 |
EYA4 | Eyes absent homolog 4 | GGATGTTTTGTTTTTATTAGAGGTATAG | AATTCTCTCAACTCAAACTCCC | GAAGGGGAAATTT | CGATATTGGAAGGAACG | +252~ +457 |
CDH13 | Cadherin 13 | AGTTTAAAGAAGTAAATGGGATGTTA | CTTCCCAAATAAATCAACAACAAC | ATTTGTTATGTAAAA | CGAGGGAGCGT | -175~ +6 |
CYP1B | Cytochrome P450 family 1 | GTTTTGATTTTGGAGTGGGAGT | CTACCCTTAAAAACCTAACAAAATC | AGGGTATGGGAATTGA | CGTTATTTATCGA | +26~ +178 |
NPY | Neuropeptide Y | GGGTTGTTTT TATTTTTGGT AGGATTAGA | CACCAAAACC CAAATATCTA CCC | AGGAAAGTAGGGAT | CGGGT ATTGTTCGAG | -353~ -253 |
VAMP8 | Vesicle-associated membrane protein 8 | AAGTTTTTGT TTGGGAAGTT ATT | CATATCTCAA AACAACCCAA | GTTAGGTGTG GTTGGAG | CGATTCGAGATGCGAGGTGG | -157~ +56 |
CASP8 | Caspase 8 | GAAGTTTGATTTTGTTGGTTTAAAA | CAACCTCTCTAACTAAACCCTCCTT | TGTTTAGAGGTTG | CGGGTTGCGGGT | +431~ +533 |
SPP1 | Secreted phosphoprotein 1 | GGAATAAGGA TAGGTAGGT | CAAAATAACT ACTTAAAAAA ACTACTTCAA | GAATAAGGAT AGGTAGGTTG GG | CGATTTGTTTAAGGTTGTAT | +99~ +117 |
CAPG | Capping protein | GGGGTAGGTTGGAAGGAAGA | ACAACCACCCTACCACCTTCA | GTTGGAAGGAAGA | CGAATTTACGAAGT | +200~+294 |
RIPK3 | Receptor-interacting serine-threonine kinase 3 | GTTTTTGGAA GGTGAGGAT | AAAACTAATA CCTTTCTCCT TAACT | ATTTAATT TGGTTG | CGGT AGGTGTTTAG GAAACG | -137~ -27 |
IFNG | Interferon gamma receptor 1 | AATAGTATTTGTTTGTGGTTGAA | TAACACCAAATCTCAAAATAACT | GAAAATGATTGAATAT | CGATTTG | +257~ +359 |
HLADPA1 | Major histocompatibility complex, class II, DP alpha 1 | AATTTTGAAAATGAATTGTGAATTG | CATTCTCTATTACTAAATAAAAAAAAC | GAGTTTTTTTGATTA | CGTTGGTA | -74~ +38 |