Dinh Diep

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Revision as of 00:37, 21 March 2012 by >Dinh
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Most recent meeting notes

  • [1] Updated March 16, 2012

Current Projects / Table of contents

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 :(

Collaborations

  • GA - (Glaucoma and optic atrophy?) (Kang Zhang lab)
    • BSPP (Noi): [39] Noi did the experiment while also training two postdocs from Kang's lab.
[40] mQTL on 30 samples, SOM analysis
[41] PCA and HClust
  • Schizophrenia (UCLA, Tina and Dr. Roel)
    • BSPP (Noi): [42] Noi did the experiment while also training Tina over the summer.
Sample identity - males versus females, [43]
Family background substraction, [44]
SibPair using TTest with family null data, [45]
Overlap SibPair with MPO, [46]
SNP Genetic distance plot, [47]


  • African Diversity - 48 Methylomes (UPenn collaboration, Sara/Laura)
    • BSPP (Noi):[48] 1st batch [49] 2nd batch, tried to improve QC but they were all too low compared to previously assayed samples.
[50] Analysis with EIGENSTAT software (population structure)
[51] PCA
[52] mQTL
[53] Cleaning and repeat PCA
[54] Checking for reference genome bias
  • N37 individual, multiple tissues (Standard, Billy Li)
    • BSPP (Noi):[55] 1st batch
[56] Genic methylation and expression levels
  • 5fC/5caC DIP-seq (University of Northern Carolina Medical School , Yi/Hao/Li)
    • Barcoding and sequencing by Alan:
[57] Genes Region Enrichment analysis, Biotin-labeled dIP 
[58] Antibody dIP
[59] [60][61] Analysis at repeats
[62] 24 sets BOWTIE mapping
[63] [64] [65] [66] BWA PE mapping and peak calling
[67] RNA-seq - repeats mapping
  • Immunogeneticity and reprogramming (Yang Xu lab)
[69] [70] Memory/mutation calling
[71] Compare WGBS


  • Breast Cancer and Diet (Richard, Moores Cancer Center UCSD)
    • Experiments were done in December 2009, January 2010, and February 2010.
[72] Paired Chi-square test 
[73] [74] Compared resequenced datasets with old
[75] [76] mQTL
  • Methylation and metabolic genes
[77] Calculate DMS
  • Memory/Mutation of iPSCs (Salk - Juan Carlos Lab, Sergio)
    • BSPP (Noi): [78] 2nd batch (MSCs, hESCs) [79] 3rd batch, after differentiation
    • BSPP with N2 protocol (Dinh): [80], [81] 1st batch
[82] Memory/mutation calling
[83] CpG localization 
[84] [85] Localization with ChIP data


Finished/dropped projects

Slides

  • [87] 8-26-09 thru 9-28-09 Slides
  • [88] October 26, 2009 Slides
  • [89] November 23, 2009 Slides
  • [90] January 25, 2010 (short slides)
  • [91] March 8, 2010 CpG Methylation

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

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<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>