Dinh Diep: Difference between revisions
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===Projects with Collaborators=== | ===Projects with Collaborators=== | ||
* '''HAPMAP Study''' (Zhang lab, on grant proposal) | |||
**BSPP (Noi): [http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-16] | |||
**WGBS (Alan): ask Alan | |||
* '''GA - (Glaucoma and optic atrophy?)''' (Kang Zhang lab) | * '''GA - (Glaucoma and optic atrophy?)''' (Kang Zhang lab) | ||
**BSPP (Noi): [http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#July_8.2C_2011.2C_gDNA_from_the_blood_samples_of_control_and_GA_patients_from_Kang_Zhang.27s_lab.2C_UCSD] Noi did the experiment while also training two postdocs from Kang's lab. | **BSPP (Noi): [http://genome-tech.ucsd.edu/LabNotes/index.php/noi:Sample_tracking#July_8.2C_2011.2C_gDNA_from_the_blood_samples_of_control_and_GA_patients_from_Kang_Zhang.27s_lab.2C_UCSD] Noi did the experiment while also training two postdocs from Kang's lab. |
Revision as of 23:14, 21 March 2012
Daily Lab Notebook
Most recent meeting notes
- [1] BSPP Meeting (Updated March 16, 2012)
Current Projects and Progress
Dinh's Projects
- bisReadMapper_v1
Developments: Dealing with WGBS data [2] GM12878
- Bisulfite Patch PCR (w/Michelle)
[3] Design [4] Consider SNPs
- DMR330K probes
re-normalization: [5] Specificity measures, [6] Probes efficiency measures, [7] [8] Resubsetting strategy, 9 Technical Replicates: [9] QC values, [10] [11] [12] Simulation of STDEV, Random tagging of probes: [13] [14] [15] Design new probes: [16] HMM to determine UMR, LMR, and HMR
- Protocol optimizations:
[17] [18] Capture with 30K, [19] Capture with 97KA/B [20] Multiplexing tests [21] Multivariate capture with DMR220K [22] N2-adapter [23] [24] BSPP [25] Training [26] [27] Normalization capture [28] [29] DMR220K + EXP1-3 Supressor oligos [30] Design Probes for Single-End sequencing [31] [32] [33] Circularization of probes
- Genemapster/Meangenemachine Updates
[34] Cuda EC [35] Sanger methylation validation [36] Installed upgrades [37] New CUDA installation [38] Test SOAP3 -- doesn't work on our GPU :(
Projects with Collaborators
- HAPMAP Study (Zhang lab, on grant proposal)
- BSPP (Noi): [39]
- WGBS (Alan): ask Alan
- GA - (Glaucoma and optic atrophy?) (Kang Zhang lab)
- BSPP (Noi): [40] Noi did the experiment while also training two postdocs from Kang's lab.
[41] mQTL on 30 samples, SOM analysis [42] PCA and HClust
- Schizophrenia (UCLA, Tina and Dr. Roel)
- BSPP (Noi): [43] Noi did the experiment while also training Tina over the summer.
Sample identity - males versus females, [44] Family background substraction, [45] SibPair using TTest with family null data, [46] Overlap SibPair with MPO, [47] SNP Genetic distance plot, [48]
- African Diversity - 48 Methylomes (UPenn collaboration, Sara/Laura)
[51] Analysis with EIGENSTAT software (population structure) [52] PCA [53] mQTL [54] Cleaning and repeat PCA [55] Checking for reference genome bias
- N37 individual, multiple tissues (Standard, Billy Li)
- BSPP (Noi):[56] 1st batch
[57] Genic methylation and expression levels
- 5fC/5caC DIP-seq (University of Northern Carolina Medical School , Yi/Hao/Li)
- Barcoding and sequencing by Alan:
[58] Genes Region Enrichment analysis, Biotin-labeled dIP [59] Antibody dIP [60] [61][62] Analysis at repeats [63] 24 sets BOWTIE mapping [64] [65] [66] [67] BWA PE mapping and peak calling [68] RNA-seq - repeats mapping
- Immunogeneticity and reprogramming (Yang Xu lab)
- BSPP (Noi):[69]
[70] [71] Memory/mutation calling [72] Compare WGBS
- Breast Cancer and Diet (Richard, Moores Cancer Center UCSD)
- Experiments were done in December 2009, January 2010, and February 2010.
[73] Paired Chi-square test [74] [75] Compared resequenced datasets with old [76] [77] mQTL
- Methylation and metabolic genes
[78] Calculate DMS
- Memory/Mutation of iPSCs (Salk - Juan Carlos Lab, Sergio)
[83] Memory/mutation calling [84] CpG localization [85] [86] Localization with ChIP data
Finished/dropped projects
- [87] Meeting notes/work for Nature Methods paper revision
- Bisulfite Sequencing of CpG Sites (w/ Jie)
- Insertional Mutagenesis, Sequencing of HIV Insertion Site (w/ Sam & Kyle)
- bwalnGPU
- Learn 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.
Slides
most recent ones at bottom
- File:GPU Project 9-28-09.pdf 8-26-09 thru 9-28-09 Slides
- File:Dinh-Presentation October 26, 2009.pdf October 26, 2009 Slides
- File:Dinh Presentation November 23, 2009.pdf November 23, 2009 Slides
- File:Lab Meeting Jan 25 2010.pdf January 25, 2010 (short slides)
- File:March 8 2010 Lab Meeting.pdf 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