Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat

Wong, Nicholas C.; Pope, Bernard J.; Candiloro, Ida; Korbie, Darren; Trau, Matt; Wong, Stephen Q.; Mikeska, Thomas; van Denderen, Bryce J. W.; Thompson, Erik W.; Eggers, Stefanie; Doyle, Stephen R.; Dobrovic, Alexander

doi:10.1186/s13742-015-0098-x

GigaScience

Table 2 Bisulfite PCR primers used in this study

From: Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat

Primer name	Primer sequence	Primer Tm	Genomic location (hg38)
mandatory01_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGAGAAGTTTGGTYGTTGYGTTTTTAT	60.1–62.9
mandatory01_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGRAAACCRCTCRCRAAATACCCTA	57.6–64.6	chr4:154710460-154710544
mandatory02_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTAGYGGAGTTTAAGGGTTAGTGT	59.2–60.9
mandatory02_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAACRAAACRCACRTACRTATATTTATA	56.3–62.1	chr1:110052409-110052486
mandatory03_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTGTTTGTTAGTTAGTTTTAGGTTTTTTAAT	59.8
mandatory03_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCTACCAAATTTCTATTACAAACCAAA	60.8	chr4:7526639-7526703
mandatory04_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGATTTGGTTTYGAGAGTTTGGATTTT	60.1–61.7
mandatory04_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAAAAACCRCACACCTAAACACTTAAA	60.1–61.7	chr2:164593225-164593299
mandatory05_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGGAATTTTGAGATTTTTAAAAGTTTTTTT	59.8
mandatory05_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATAAAAACAACAAATACCACTTCCTAAA	59.9	chr2:9518296-9518358
mandatory06_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTGYGTYGATTTTGGTTTTGGTTAT	57.6–60.9
mandatory06_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCRACCCCTCCCAAATCCTAAAA	60.1–62.1	chr17:80709100-80709203
mandatory07_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGTTAGAGGAGAYGTTTTAGTTTTT	59.2–60.9
mandatory07_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCAATTCCAAAAAACRTCAATCACAATAA	59.9–61.5	chr3:142837969-142838050
mandatory08_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGTTAAGAGGAGTTTGTTTTGTTTTAT	60.8
mandatory08_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTTTCACTAAAAAACCTCACTCCCTA	60.9	chr7:140218100-140218192
mandatory09_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTTTAGAGTGTTTTTGGTTTTATTATTTTT	60.2
mandatory09_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTATTTACCCCTAAAAATACCCTTTATA	59.2	chr7:26206542-26206614
mandatory10_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGAAGTTGAAGTGAGAATGTGATT	60.3
mandatory10_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAATACCCATACAAACTATCTACACAA	60.1	chr7:3025554-3025664
mandatory11_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTATATAAAAATTATTAAGAATTTTATTGTTTTGT	58.5
mandatory11_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAATATAACCAAAATCCAAATAACACTAA	58.2	chr7:138229946-138230021
mandatory12_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGYGGYGTTTGATGGATTTGGTTT	59.2–62.9
mandatory12_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCTTAATATAACCTAAACCCATATACTA	59.2	chr2:42275714-42275789
mandatory13_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTAGATTATGTTAAGGATTTTGGAAAT	59.2
mandatory13_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCTATACTATCAACACCCATTACTTAA	60.8	chr15:100249155-100249220
mandatory14_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTAAATTAGATGAGGTATAGTAGATTATAT	59.2
mandatory14_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCAACTCTATCTCAAACTTCAAAAAATA	59.2	chr4:147557821-147557938
mandatory15_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTGGGGGATAGTTTTGGGTAT	60.1
mandatory15_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTACAACCTCCTACAAAAAAACCCTA	60.9	chr17:75369174-75369252
mandatory16_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATATTTTTAATTTAATTTGAAGGTTTATTGT	57.8
mandatory16_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCCAAACTTTCTCCTATAATCCAA	60.3	chr7:93520244-93520332
h19_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTTGTATTATTTTTTTTTTTGAGAGTTTATTT	60.2
h19_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATACRAAAAAAACCCACAATAAACTTAATA	59.8–61	chr11:2017873-2018050
mest_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGTTTTGTTTTTTTAATTGTGTTTATTGTTT	60.2
mest_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTAACCACTATAACCAAAATTACACAAAA	59.9	chr7:130131098-130131299
xist_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTAGTAATTTAGTATTGTTTATTTTATTTTTTT	59
xist_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATAACRAACCTCTTTATCTTTACTATATA	59.2–60.5	chrX:73070975-73071183
runx3_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTTAGAYGTTYGGAGTTTTAGGGT	58.3–62
runx3_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCRACAACCCCAACTTCCTCTA	59.5–61.2	chr1:25256022-25256153
rarb_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAATTTTTTTATGYGAGTTGTTTGAGGAT	59.9–61.5
rarb_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCTCCTTCCAAATAAATACTTACAAAAAA	59.9	chr3:25469822-25469959
mlh1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGYGGGAGGTTATAAGAGTAGGGTT	60.9–62.9
mlh1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATACRAAATATCCAACCAATAAAAACAAAA	59.8–61	chr3:37034573-37034734
rassf1a_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTTTYGTAGTTTAATGAGTTTAGGTTTT	60.5–62.1
rassf1a_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAATCCCTACACCCAAATTTCCATTA	60.9	chr3:50378200-50378398
apc_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGAGAGAGAAGTAGTTGTGTAAT	60.3
apc_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCATTCTATCTCCAATAACACCCTAA	60.9	chr5:112073447-112073596
cdkn2a_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTTTGTTTTTTAAATTTTTTGGAGGGAT	59.2
cdkn2a_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCCAACCTAAAACRACTTCAAAAATA	60.1–61.7	chr9:21974960-21975097
dapk1_p1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTTYGGAGTGTGAGGAGGATAGT	60.9–62.9
dapk1_p1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGRACRACRAAAACACAACTAAAAAATAAATA	58.5–62.6	chr9:90112783-90112938
dapk1_p2_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGYGGAGGGATYGGGGAGTTTTT	62.1–65.5
dapk1_p2_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCRCCTTAACCTTCCCAATTA	63.6–65.2	chr9:90112991-90113144
dapk1_i1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGAGGYGGGGAGGTTAGTTAT	61.2–63.2
dapk1_i1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAAATAAAAAAAAACACCCTTTATTAAAACTAA	59.8	chr9:90113588-90113759
gstp1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTTGGGAAAGAGGGAAAGGTTTTT	60.3
gstp1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGRCRACCTCCRAACCTTATAAAAATAA	58.4–62.9	chr11:67351064-67351273
cdh1_snp_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTTTAGTAATTTTAGGTTAGAGGGTT	59.2
cdh1_snp_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAAAAATAAATACRTAACTACAACCAAATAAA	59–60.2	chr16:68771006-68771197
cdh1_3ê_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTYGGAATTGTAAAGTATTTGTGAGT	60.1–61.7
cdh1_3ê_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATCAAAAAATCCRAAATACCTACAACAA	59.5–61.5	chr16:68771201-68771385
brca1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTTAGTTATTTGAGAAATTTTATAGTTTGTT	59
brca1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAATTTCRTATTCTAAAAAACTACTACTTAA	58.5–59.8	chr17:41277330-41277493
AluSx_1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAGATTAGTTTGGTTAATATGGTGAAATT	59.9
AluSx_1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCTCTATCRCCCAAACTAAAATACAATA	60.8–62.1
AluSx_2_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTTGTAATTTTAGTATTTTGGGAGGT	60.8
AluSx_2_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAACCTCCCRAATAACTAAAACTACAA	60.1–61.7
L1ME_ORF2_1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATGATAAAAGGGTTAATTTATTAGAAAGAT	59.8
L1ME_ORF2_1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCTATCTAATTATTCTRTCAATTACTAAAAA	58.5–59.8
L1ME_ORF2_2_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGATTGATAAAGAAGAAAATAGATAAGATAT	59.8
L1ME_ORF2_2_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCTATTCAAATTTTCTATTTCTTTTTAAATCAA	59.8
foxe3_2_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTTTGGGGAGGTTTATTTGAGGT	59.2
foxe3_2_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAACRCAAAATATACTCCAAACCAAAATA	59.9–61.5	chr1
foxp3_1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTTGGGTTTAGGGTTTTATTTGTAGT	59.2
foxp3_1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGACCCAAAACCTCAAACCTACTAAA	60.3	chrX
foxp3_2_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTTTTGGGGATGGGTTAAGGGTT	60.9
foxp3_2_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCAACCAATACCTACTTTAACCAAAAA	60.1	chrX
tlx3_1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTYGGTTTAAGAAAGATGATATAGAGTT	59.9–61.5
tlx3_1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCCATCCTAAACRAACRAAAAAACTAA	59.2–62.1	chr5
tlx3_2_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGYGTTAGTTATTTGGGAGGGTTT	59.2–60.9
tlx3_2_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAACRCTAAACTCAAATTCACACTATAAA	59.5–61.5	chr5
uniq_noCG_1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGAGTTATGTAGTTTTAGTTAGAAGTTT	59.2
uniq_noCG_1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAAATCTAAATTTTAACACCTAAAACTATTTTAA	59.8	chr5
uniq_noCG_2_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATATGAAAGGTTGGTTTTATTGTTGAAT	59.9
uniq_noCG_2_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAAAATAAACTTAATAACTCTACTCTTATATA	59	chr5
mgmt_1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTGAGTTAGGTTTTGGTAGTGTT	60.3
mgmt_1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCTAATACCRCTCCCCTAATCAAAA	60.3–62	chr10
mgmt_2_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTGGTAGTTTYGAGTGGTTTTGT	59.2–60.9
mgmt_2_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAACTAAACAACACCTAAAAAACACTTAA	59.9	chr10
mito_1_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTATTTATTTTTAATAGTATATAGTATATAAAGTT	58.5
mito_1_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGACTTTAACTACCCCCAAATATTATAA	58.4	chrM
mito_2_plus_F	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATGATTTTTAATAGGGGTTTTTTTAGTTT	59.2
mito_2_plus_R	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCRTATCRAAAACCTTTTTAAACAAATAATA	58.5–61	chrM

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ISSN: 2047-217X

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