Nongluk (Noi) Plongthongkum: Difference between revisions

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= [[Noi:DMR220k LabNotes | Labnote]] =
= [[Noi:Sample tracking | Sample tracking]] =
= [[Noi:Sample tracking | Sample tracking]] =
= Current Projects =
= Current Projects =


*[[Noi:Targeted bisulfite sequencing|Targeted bisulfite sequencing]]  
== [[Noi:Targeted bisulfite sequencing|Targeted bisulfite sequencing]] ==
** '''Schizophrenia''' (UCLA, Roel Ophoff):  
* '''Schizophrenia''' (UCLA, Roel Ophoff):  
*** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-14]]
** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-14]]
*** Mapping
** Mapping
**** Batch4: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-1-2]]
*** Batch4: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-1-2]]
*** Sample identity check by Dinh (checked after combining three batches of sequencing data):  
** 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: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-28]]
*** Homozygous SNPs and heterozygous SNPs call for X chromosome to identify males vs. females: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-28]]
**** Genetic distance: [[http://genome-tech.ucsd.edu/LabNotes/index.php/File:UCLA_GeneticDistance.pdf]]
*** Genetic distance: [[http://genome-tech.ucsd.edu/LabNotes/index.php/File:UCLA_GeneticDistance.pdf]]
*** Mid-parent offspring (mpo) analysis
** Mid-parent offspring (mpo) analysis
**** Preliminary result by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2011-9-27]]
*** Preliminary result by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2011-9-27]]
**** Analysis of combining data (4 batches of sequencing data): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-19]]
*** Analysis of combining data (4 batches of sequencing data): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-19]]
*** mQTL analysis: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-1-24]]
** mQTL analysis: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-1-24]]
*** ASM analysis: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-21]]
** ASM analysis: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-21]]
*** Regression analysis:
** Regression analysis:
** '''Geographic Astrophy (GA)''' (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
* '''Geographic Astrophy (GA)''' (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
*** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-7-28]] --> note: this experiment failed in amplification step [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-9]]
** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-7-28]] --> note: this experiment failed in amplification step [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-9]]
*** Regression analysis by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2011-10-14]]
** Regression analysis by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2011-10-14]]
**'''HAPMAP project''' (HAPMAP PT01, two families, 1362 and 1464)
* '''HAPMAP project''' (HAPMAP PT01, two families, 1362 and 1464)
*** BSPP capture:  
** BSPP capture:  
*** Mapping statistic: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-2-2]]
** Mapping statistic: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-2-2]]
*** ASM analysis:  
** ASM analysis:  
**** Preliminary analysis of sequence-dependent ASM: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-2-15#On_ASM_output_data]]
*** Preliminary analysis of sequence-dependent ASM: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-2-15#On_ASM_output_data]]
**** Sequence dependent test by Dinh: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-3-21]]
*** Sequence dependent test by Dinh: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-3-21]]
** '''Randomly tagging primers''' (with Athurva and Dinh)
* '''Randomly tagging primers''' (with Athurva and Dinh)
*** PCR condition optimization: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-1]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-2#PCR_set_up]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-4#Part_III]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-5]]
** PCR condition optimization: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-1]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-2#PCR_set_up]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-4#Part_III]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-5]]
*** Colony PCR and sequence verification by Sanger's sequencing: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-7]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-13]]
** Colony PCR and sequence verification by Sanger's sequencing: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-7]] [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-13]]


*[[Noi:Library construction|Library construction (with Dinh)]]
== [[Noi:Library construction|Library construction (with Dinh)]] ==
 
= 2012 =
<calendar>
name=Noi DMR220 LabNotes
format=%name/NOTES/%year-%month-%day
date=2012/01/01
view=oneyear
</calendar>
= 2011 =
<calendar>
name=Noi DMR220 LabNotes
format=%name/NOTES/%year-%month-%day
date=2011/01/01
view=oneyear
</calendar>
= 2010 =
<calendar>
name=Noi DMR220 LabNotes
format=%name/NOTES/%year-%month-%day
date=2010/10/01
view=oneyear
</calendar>

Revision as of 19:07, 22 March 2012

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:
  • Geographic Astrophy (GA) (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
    • BSPP capture: [[9]] --> note: this experiment failed in amplification step [[10]]
    • Regression analysis by Dr. Zhang: [[11]]
  • HAPMAP project (HAPMAP PT01, two families, 1362 and 1464)
    • BSPP capture:
    • Mapping statistic: [[12]]
    • ASM analysis:
      • Preliminary analysis of sequence-dependent ASM: [[13]]
      • Sequence dependent test by Dinh: [[14]]
  • Randomly tagging primers (with Athurva and Dinh)
    • PCR condition optimization: [[15]] [[16]] [[17]] [[18]]
    • Colony PCR and sequence verification by Sanger's sequencing: [[19]] [[20]]

Library construction (with Dinh)