Nongluk (Noi) Plongthongkum: Difference between revisions
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** 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]] | ||
* '''ASM analysis of WGBS of NA12878''' | |||
=== Protocols === | === Protocols === | ||
* '''Probe preparation''' | * '''Probe preparation''' | ||
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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]] | ||
== [[Noi:Library construction|Library construction (with Dinh)]] == | == [[Noi:Library construction|Library construction (with Dinh)]] == |
Revision as of 19:19, 26 March 2012
Labnote
Sample tracking
Current Projects
Targeted bisulfite sequencing
- Parkinson's disease (PD) data set from Burnham Institute
- Schizophrenia (UCLA, Roel Ophoff):
- Geographic Astrophy (GA) (UCSD, Kang Zhang) Note: most of the data analysis was performed by Dr. Zhang and Dinh
- BSPP capture: [[12]] --> note: this experiment failed in amplification step [[13]]
- Mapping to hg19: File:BSPP AMD-mapping-summary 2011 10 12.xlsx
- Regression analysis by Dr. Zhang: [[14]]
- HAPMAP project (HAPMAP PT01, two families, 1362 and 1464)
- Randomly tagging primers (with Athurva and Dinh)
- ASM analysis of WGBS of NA12878
Protocols
- Probe preparation
- DMR330k probe synthesized by Agilent:
- Original protocol (DMR220k) by Dr. Zhang: [[24]]
- File:DMR330k probe production.doc
- Probe synthesized by LC Sciences
- DMR330k probe synthesized by Agilent:
- Library construction (BSPP)