Nongluk (Noi) Plongthongkum: Difference between revisions
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** Low coverage WGBS by KAPA protocol (epMotion run): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-31]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-8-26]] | ** Low coverage WGBS by KAPA protocol (epMotion run): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-31]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-8-26]] | ||
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* '''WGBS of HAPMAP samples by KAPA protocol (epMotion run) | * '''WGBS of HAPMAP samples by KAPA protocol (epMotion run)''' | ||
** Library preparation: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-6]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-7-27]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-8-1]] | |||
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* '''LGH-Project, collaboration with Guanghui, Salk Institute''' | * '''LGH-Project, collaboration with Guanghui, Salk Institute''' |
Revision as of 00:03, 30 August 2012
Quick&Useful links
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: [[23]] --> note: this experiment failed in amplification step [[24]]
- Mapping to hg19: File:BSPP AMD-mapping-summary 2011 10 12.xlsx
- Regression analysis by Dr. Zhang: [[25]]
- Overlapping of Illumina 450k methylation array and BSPP: [[26]]
- HAPMAP project (HAPMAP PT01, two families, 1362 and 1464)
- Randomly tagging primers (with Athurva and Dinh)
- BSPP capture with probes synthesized by LC Sciences (Nature Methods 2012 paper)
- ASM analysis of WGBS of NA12878
- Concatenate fastq files as input for ASM pipeline (this step failed because less or cat command cannot print out all data into the same file: [48]
- Mapping to separate out the reads based on different chromosomes by Dinh: [[49]] --> output files on genome-miner: /media/Ext12T/DD_Ext12T/HL_WGBS_map
- ASM output data on genome-miner: /home/nplongth/Noi_scratch/ASM_WGBS.NA12878_2012_03_14
- Probe production for Hi-resolution chromosome painting project (probe production part)
- PNAS revision_May2012 (I work on 330k BSPP capture)
- ASM and ASCM in human cells project (I work on 330k BSPP capture)
- N37 sample (10 tissues from Dr. Billy Jin, Stanford)
- LGH-Project, collaboration with Guanghui, Salk Institute
- epMotion testing
Protocols
- Probe preparation
- DMR330k probe synthesized by Agilent:
- Original protocol (DMR220k) by Dr. Zhang: [[78]]
- DMR330k probe production_very details version
- [Agilent_probe_preparation]
- [LC_Sciences_probe_preparation]
- Probe synthesized by LC Sciences
- DMR330k probe synthesized by Agilent:
- Library construction (BSPP)