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]] == | |||
* '''Schizophrenia''' (UCLA, Roel Ophoff): | |||
** BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-14]] | |||
** Mapping | |||
*** 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): | |||
*** 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]] | |||
** Mid-parent offspring (mpo) analysis | |||
*** 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]] | |||
** 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]] | |||
** Regression analysis: | |||
* '''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]] | |||
** 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) | |||
** BSPP capture: | |||
** Mapping statistic: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-2-2]] | |||
** 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]] | |||
*** 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) | |||
** 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]] | |||
== [[Noi:Library construction|Library construction (with Dinh)]] == | |||
Revision as of 19:07, 22 March 2012
Labnote
Sample tracking
Current Projects
Targeted bisulfite sequencing
- Schizophrenia (UCLA, Roel Ophoff):
- 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)
- Randomly tagging primers (with Athurva and Dinh)