Dinh Diep: Difference between revisions
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** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-20] Analysis with EIGENSTAT software (population structure) | ** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-7-20] Analysis with EIGENSTAT software (population structure) | ||
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-8-29] PCA | ** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-8-29] PCA | ||
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-9-29] mQTL | |||
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-21] Cleaning and repeat PCA | ** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-21] Cleaning and repeat PCA | ||
** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-27] Checking for reference genome bias | ** [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-2-27] Checking for reference genome bias |
Revision as of 00:26, 21 March 2012
Most recent meeting notes
- [1] Updated March 16, 2012
Current Projects / Table of contents
- bisReadMapper_v1
- Developments:
- Bisulfite Patch PCR (w/Michelle)
- Memory/Mutation of iPSCs (Salk - Juan Carlos Lab, Sergio)
- BSPP (Noi):
[4] 2nd batch (MSCs, hESCs) [5] 3rd batch, after differentiation
- BSPP with N2 protocol (Dinh):
- African Diversity - 48 Methylomes (UPenn collaboration, Sara/Laura)
- BSPP (Noi):
[12] 1st batch [13] 2nd batch, tried to improve QC but they were all too low compared to previously assayed samples.
- N37 individual, multiple tissues (Standard collaboration, Billy)
- BSPP (Noi):
[19] 1st batch
- [20] Genic methylation and expression levels
- GA - (Glaucoma and optic atrophy?) (Kang Zhang lab)
- BSPP (Noi):
[21] Noi did the experiment while also training two postdocs from Kang's lab.
- Schizophrenia (UCLA, Tina and Dr. Roel)
- BSPP (Noi):
[24] Noi did the experiment while also training Tina over the summer.
- 5fC/5caC DIP-seq (University of Northern Carolina Medical School , Yi/Hao/Li)
- Immunogeneticity and reprogramming (Yang Xu lab)
- BSPP (Noi):
- Breast Cancer and Diet (Richard, Moores Cancer Center UCSD)
- Methylation and metabolic genes
- DMR330K probes
- Protocol optimizations:
- [63] [64] Capture with 30K,
- [65] Capture with 97KA/B
- [66] Multiplexing tests
- [67] Multivariate capture with DMR220K
- [68] N2-adapter
- [69] [70] BSPP [71] Training
- [72] [73] Normalization capture
- [74] [75] DMR220K + EXP1-3 Supressor oligos
- [76] Design Probes for Single-End sequencing
- [77] [78] [79] Circularization of probes
- Genemapster/Meangenemachine Updates
Old projects
- [85] Meeting notes for Nature Methods revision
- Bisulfite Sequencing of CpG Sites (w/ Jie)
- Insertional Mutagenesis, Sequencing of HIV Insertion Site (w/ Sam & Kyle)
- bwalnGPU
Slides
- [86] 8-26-09 thru 9-28-09 Slides
- [87] October 26, 2009 Slides
- [88] November 23, 2009 Slides
- [89] January 25, 2010 (short slides)
- [90] March 8, 2010 CpG Methylation
- File:7-28-10 Lab Meeting.pdf July 28, 2010 mQTL CpG-SNP distance distribution, Epigenetic Reprogramming
- File:Lab Meeting 11 10 10.pdf November 10 2010 Lab Meeting
- File:Lab Meeting 06 21 11.pdf June 21 2011 Lab Meeting
- File:Journal Club 06 28 11.pdf June 28 2011 Journal Club
- File:Journal Club 09 13 11.pdf September 13 2011 Journal Club
- File:Differential Methylation of IPSCs by Episomal Reprogramming 8 26 2011.pdf August 21 2011 DMS of iPSCs by Episomal Reprogramming
- File:Lab Meeting 08 23 11.pdf August 23 2011 Lab Meeting
- File:African Methylome QC and Coverage.pdf August 26 2011 African Methylomes QC and Average Coverage
- File:African Methylome QC and Genetics Aug31.pdf August 31 2011 African Methylomes QC and Genetics
- File:5fC DIP-seq slides 9 22 11.pdf September 22 2011 5fC DIP-seq analysis
- File:UCLA Schizophrenia Sibpair.ppt December 5 2011 Schizophrenia Sib-pair Analysis
- File:Journal Club 12 12 11.ppt December 12 2011 Journal Club
Sequencing
1. Perform quantification of libraries using PhiX 2. Perform Cluster Generation and Sequencing, Protocol 3. Run pipeline modules for image analysis, base calling, and sequence alignment.
Notebook
<calendar> name=Dinh/Dinh_2012 format=%name/NOTES/%year-%month-%day date=2012/06/22 view=oneyear </calendar>
<calendar> name=Dinh_2011 format=%name/NOTES/%year-%month-%day date=2011/06/22 view=oneyear </calendar>
<calendar> name=Dinh format=%name/NOTES/%year-%month-%day date=2010/07/01 view=oneyear </calendar>