Nongluk (Noi) Plongthongkum

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Revision as of 02:58, 24 March 2012 by >Noi
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Labnote

Sample tracking

Current Projects

Targeted bisulfite sequencing

  • Schizophrenia (UCLA, Roel Ophoff):
    • BSPP capture: [[1]]
    • Mapping
    • Sample identity check by Dinh (checked after combining three batches of sequencing data):
      • Homozygous SNPs and heterozygous SNPs call for X chromosome to identify males vs. females: [[3]]
      • Genetic distance: [[4]]
    • Mid-parent offspring (mpo) analysis
      • Preliminary result by Dr. Zhang: [[5]]
      • Analysis of combining data (4 batches of sequencing data): [[6]]
    • mQTL analysis: [[7]]
    • ASM analysis: [[8]]
    • Regression analysis: [[9]]
  • Geographic Astrophy (GA) (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
    • BSPP capture: [[10]] --> note: this experiment failed in amplification step [[11]]
    • Regression analysis by Dr. Zhang: [[12]]
  • HAPMAP project (HAPMAP PT01, two families, 1362 and 1464)
    • BSPP capture:
    • Mapping statistic: [[13]]
    • ASM analysis:
      • Preliminary analysis of sequence-dependent ASM: [[14]]
      • Sequence dependent test by Dinh: [[15]]
  • Randomly tagging primers (with Athurva and Dinh)
    • PCR condition optimization: [[16]] [[17]] [[18]] [[19]]
    • Colony PCR and sequence verification by Sanger's sequencing: [[20]] [[21]]

Protocols

  • Probe preparation
    • DMR330k probe synthesized by Agilent
    • Probe synthesized by LC Sciences

Library construction (with Dinh)