Nongluk (Noi) Plongthongkum: Difference between revisions

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** N2 adapter protocol: Related experiment --> [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-18]]
** N2 adapter protocol: Related experiment --> [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-18]]
** Library-free protocol: Related experiment --> [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-28]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-6-6]]
** Library-free protocol: Related experiment --> [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-28]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-6-6]]
** '''ASM analysis of WGBS of NA12878'''
== [[Noi:Library construction|Library construction (with Dinh)]] ==
== [[Noi:Library construction|Library construction (with Dinh)]] ==

Revision as of 19:18, 26 March 2012

Labnote

Sample tracking

Current Projects

Targeted bisulfite sequencing

  • Parkinson's disease (PD) data set from Burnham Institute
    • BSPP capture: [[1]]
    • Mapping to hg18 (CpG): [[2]]
    • Mapping to hg19 (CpG and non-CpG):
  • Schizophrenia (UCLA, Roel Ophoff):
    • BSPP capture: [[3]]
    • 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: [[5]]
      • Genetic distance: [[6]]
    • Mid-parent offspring (mpo) analysis
      • Preliminary result by Dr. Zhang: [[7]]
      • Analysis of combining data (4 batches of sequencing data): [[8]]
    • mQTL analysis: [[9]]
    • ASM analysis: [[10]]
    • Regression analysis: [[11]]
  • Geographic Astrophy (GA) (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
  • HAPMAP project (HAPMAP PT01, two families, 1362 and 1464)
    • BSPP capture:
    • Mapping to hg19: [[15]]
    • ASM analysis:
      • Preliminary analysis of sequence-dependent ASM: [[16]]
      • Sequence dependent test by Dinh: [[17]]
  • Randomly tagging primers (with Athurva and Dinh)
    • PCR condition optimization: [[18]] [[19]] [[20]] [[21]]
    • Colony PCR and sequence verification by Sanger's sequencing: [[22]] [[23]]

Protocols

  • Probe preparation
    • DMR330k probe synthesized by Agilent:
    • Probe synthesized by LC Sciences
      • Reference protocol: [25]
      • Adjusted protocol and related experiment: [[26]]
  • Library construction (BSPP)
    • N2 adapter protocol: Related experiment --> [[27]]
    • Library-free protocol: Related experiment --> [[28]] [[29]]
    • ASM analysis of WGBS of NA12878

Library construction (with Dinh)