Kun:LabNotes/ExonomeSeq/2009-11-22

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Revision as of 19:33, 22 November 2009 by KunZhang (talk | contribs) (New page: ==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...)
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Additional Sanger confirmation of mutations[edit]

  • 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.
Primer ID Sequence Primer ID Sequence 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