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Kun:LabNotes/ExonomeSeq/2009-11-22
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==Additional Sanger confirmation of mutations== *I used the reads that came from the CV-fibroblast library Alice made on 10/09/09 as the reference to call variants in the HL022 CV-iPS data. The CV-fibroblast library was suboptimal, so I filtered out all synonymous variants, and manually check each candidate in the HuRef database. Eventually I found 12 candidates, for which the PCR primers were designed and ordered. *Athurva also performed variant calling independently, and found three additional candidates that were not in my list. These three candidates were also included in the Sanger validation. {| {{table}} | align="center" style="background:#f0f0f0;"|'''Primer ID''' | align="center" style="background:#f0f0f0;"|'''Sequence''' | align="center" style="background:#f0f0f0;"|'''Primer ID''' | align="center" style="background:#f0f0f0;"|'''Sequence''' | align="center" style="background:#f0f0f0;"|'''Amplicon Info''' |- | USP54-S252F-LP||TAGGCAGCCCAGAGTTTAAG||USP54-S252F-RP||TTGTGCTTCACTGTCCTGAT||>chr10:74946544+74946945 402bp |- | PSMG1-M88T-LP||CCTACCGAGGGATTGGATTT||PSMG1-M88T-RP||TATTACCCCGTGAGCATGTG||>chr21:39474076+39474498 423bp |- | CDKN2AIP-S330L-LP||CACGGTTCTGCATCATTTGT||CDKN2AIP-S330L-RP||GCTGCTCTTGGAAGCTAGTA||>chr4:184604546+184604959 414bp |- | GSG1-V252I-LP||AGATGCCTACCTCCATTCTT||GSG1-V252I-RP||ATTCTCCCCTTCTCAGATGC||>chr12:13131979+13132379 401bp |- | SPEN-L929*-LP||GAGAGCAAAGCCCTGAAAAG||SPEN-L929*-RP||TCCAGATCCACAGCACTTAC||>chr1:16127853+16128258 406bp |- | PBLD-R81*-LP||ACTAGGCTCAGGTTTGATTCT||PBLD-R81*-RP||CTAGACCTCAGCAACCCAAA||>chr10:69721742+69722146 405bp |- | OR6Q1-L305V-LP||AGACTGTGGATTTCCTGGTG||OR6Q1-L305V-RP||ATATCCAAGGCAAGGAAACT||>chr11:57555599+57555992 394bp |- | KIAA0564-I963L-LP||CACAACCACACACTGTGAAA||KIAA0564-I963L-RP||TTCAGTCACCCAGTGAAGTT||>chr13:41156992+41157383 392bp |- | ZWILCH-N56H-LP||TTCCATTGACTTGCATAGAACT||ZWILCH-N56H-RP||AGAACTCATTTTCACCGATGC||>chr15:64593287+64593586 300bp |- | TIAM1-K1469R-LP||TTCACGGACTCACAGAACTC||TIAM1-K1469R-RP||ATGCTCCATGACAGATTGGT||>chr21:31414786+31415195 410bp |- | DSP-M2819I-LP||GCTATGCCAAAATCCTGACC||DSP-M2819I-RP||CAAGCACCGGGATTTTCTTT||>chr6:7530800+7531199 400bp |- | RNF20-R415K-LP||AGTCACAGTTCTCCGTCTTG||RNF20-R415K-RP||TCTCACATACACGTAAGCTCT||>chr9:103352770+103353351 582bp |- | STK33-V270L-LP||TGGCAAAAATTGTTCAAGCTG||STK33-V270L-RP||GAACCCCAGAATTCAATGCAA||>chr11:8430558+8431132 575bp |- | OR13F1-S229G-LP||CTGCCATGGTGGAAATGATG||OR13F1-S229G-RP||AGGATTCAACATGGGGGTTT||>chr9:106306828+106307225 398bp |- | GOLGA4-G1943D-LP||ACAGGCTTTACAACAGATGGA||GOLGA4-G1943D-RP||TGGGTTGGTGAAACTTATCC||>chr3:37344033+37344432 400bp |- | |}
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