Dinh Diep: Difference between revisions

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==Daily Lab Notebook==
* * [[Dinh/Daily|Notebook]]
==Most recent meeting notes==
==Most recent meeting notes==
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-27] BSPP Meeting (Updated March 16, 2012)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-27] BSPP Meeting (Updated March 16, 2012)
==Current Projects / Table of contents==
==Current Projects / Table of contents==
===Dinh's Projects===
===Lab Projects===
* '''bisReadMapper_v1'''
* '''bisReadMapper_v1'''
  Developments:
  Developments:
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  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-7#SOAP3_.28latest_version.29] Test SOAP3 -- doesn't work on our GPU :(
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-7#SOAP3_.28latest_version.29] Test SOAP3 -- doesn't work on our GPU :(


===Collaborations===
===Projects with Collaborators===
* '''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.
Line 49: Line 51:
  Overlap SibPair with MPO, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30]
  Overlap SibPair with MPO, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30]
  SNP Genetic distance plot, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30]
  SNP Genetic distance plot, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-30]


* '''African Diversity - 48 Methylomes''' (UPenn collaboration, Sara/Laura)
* '''African Diversity - 48 Methylomes''' (UPenn collaboration, Sara/Laura)
Line 76: Line 77:
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-17] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-1] Memory/mutation calling
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-17] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-1] Memory/mutation calling
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-13] Compare WGBS
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-13] Compare WGBS


* '''Breast Cancer and Diet''' (Richard, Moores Cancer Center UCSD)
* '''Breast Cancer and Diet''' (Richard, Moores Cancer Center UCSD)
Line 93: Line 93:
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-9] CpG localization  
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-9] CpG localization  
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-4] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-6] Localization with ChIP data
  [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-4] [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2012/NOTES/2012-1-6] Localization with ChIP data


===Finished/dropped projects===
===Finished/dropped projects===
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-7] Meeting notes for Nature Methods revision
* [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-10-7] Meeting notes/work for Nature Methods paper revision
* [[dinh:LAB/Bisulfite_Sequencing|Bisulfite Sequencing of CpG Sites (w/ Jie)]]
* [[dinh:LAB/Bisulfite_Sequencing|Bisulfite Sequencing of CpG Sites (w/ Jie)]]
* [[dinh:COMPUTATIONAL/HIV_Insertion_Site_Sequencing| Insertional Mutagenesis, Sequencing of HIV Insertion Site (w/ Sam & Kyle)]]
* [[dinh:COMPUTATIONAL/HIV_Insertion_Site_Sequencing| Insertional Mutagenesis, Sequencing of HIV Insertion Site (w/ Sam & Kyle)]]
* [[dinh:COMPUTATIONAL/GPU_Project|bwalnGPU]]
* [[dinh:COMPUTATIONAL/GPU_Project|bwalnGPU]]
* Learn sequencing
1. Perform quantification of libraries using PhiX
2. Perform Cluster Generation and Sequencing, [http://genome-tech.ucsd.edu/LabNotes/upload/7/71/Dinh_All_In_One_Cluster_Generation.doc Protocol]
3. Run pipeline modules for image analysis, base calling, and sequence alignment.


==Slides==
==Slides==
'''most recent ones at bottom'''
* [http://genome-tech.ucsd.edu/LabNotes/upload/b/b9/GPU_Project_9-28-09.pdf] 8-26-09 thru 9-28-09 Slides
* [http://genome-tech.ucsd.edu/LabNotes/upload/b/b9/GPU_Project_9-28-09.pdf] 8-26-09 thru 9-28-09 Slides
* [http://genome-tech.ucsd.edu/LabNotes/upload/b/b5/Dinh-Presentation_October_26,_2009.pdf] October 26, 2009 Slides
* [http://genome-tech.ucsd.edu/LabNotes/upload/b/b5/Dinh-Presentation_October_26,_2009.pdf] October 26, 2009 Slides
* [http://genome-tech.ucsd.edu/LabNotes/upload/d/d2/Dinh_Presentation_November_23%2C_2009.pdf] November 23, 2009 Slides
* [http://genome-tech.ucsd.edu/LabNotes/upload/d/d2/Dinh_Presentation_November_23%2C_2009.pdf] November 23, 2009 Slides
* [http://genome-tech.ucsd.edu/LabNotes/upload/0/0c/Lab_Meeting_Jan_25_2010.pdf] January 25, 2010 (short slides)
* [http://genome-tech.ucsd.edu/LabNotes/upload/0/0c/Lab_Meeting_Jan_25_2010.pdf] January 25, 2010 (short slides)
* [http://genome-tech.ucsd.edu/LabNotes/index.php/File:March_8_2010_Lab_Meeting.pdf] March 8, 2010 CpG Methylation
* [http://genome-tech.ucsd.edu/LabNotes/index.php/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: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_11_10_10.pdf]] November 10 2010 Lab Meeting
* [[File:Lab_Meeting_06_21_11.pdf]] June 21 2011 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_06_28_11.pdf]] June 28 2011 Journal Club  
* [[File:Journal_Club_09_13_11.pdf]] September 13 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: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: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_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: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: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:UCLA_Schizophrenia_Sibpair.ppt]] December 5 2011 Schizophrenia Sib-pair Analysis
*[[File:Journal_Club_12_12_11.ppt]] December 12 2011 Journal Club
*[[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, [http://genome-tech.ucsd.edu/LabNotes/upload/7/71/Dinh_All_In_One_Cluster_Generation.doc Protocol]
3. Run pipeline modules for image analysis, base calling, and sequence alignment.
=Notebook=
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<calendar>
name=Dinh_2011
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date=2011/06/22
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<calendar>
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date=2010/07/01
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Revision as of 00:46, 21 March 2012

Daily Lab Notebook

Most recent meeting notes

  • [1] BSPP Meeting (Updated March 16, 2012)

Current Projects / Table of contents

Lab 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

  • 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

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