Nongluk (Noi) Plongthongkum: Difference between revisions
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** 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]] | ||
== Protocols == | == Protocols == | ||
* Probe preparation | * '''Probe preparation''' | ||
** DMR330k probe synthesized by Agilent: | ** DMR330k probe synthesized by Agilent: | ||
*** Original protocol (DMR220k) by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2010-6-8]] | *** Original protocol (DMR220k) by Dr. Zhang: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/CpgSeq/2010-6-8]] | ||
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*** Reference protocol: [http://arep.med.harvard.edu/pdf/Porreca07.pdf] | *** Reference protocol: [http://arep.med.harvard.edu/pdf/Porreca07.pdf] | ||
*** Adjusted protocol and related experiment: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-6]] | *** Adjusted protocol and related experiment: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-6]] | ||
* Library construction (BSPP) | * '''Library construction (BSPP)''' | ||
** N2 adapter protocol: | ** N2 adapter protocol: | ||
** Library-free protocol: | ** Library-free protocol: | ||
== [[Noi:Library construction|Library construction (with Dinh)]] == | == [[Noi:Library construction|Library construction (with Dinh)]] == |
Revision as of 21:07, 24 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)
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)
- N2 adapter protocol:
- Library-free protocol: