Dinh Diep: Difference between revisions

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>Dinh
>Dinh
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===Dinh's Projects===
===Dinh's Projects===
* ''' MONOD '''
* ''' MONOD '''
   BSPP & SeqCap Mapping statistics: [[File:Dinh:150209_SN216_MONOD.xlsx]]
   BSPP & SeqCap Mapping statistics: [[File:150209_SN216_mapping_summary_statistics.xlsx]]
* ''' 5hmC Experiments '''
* ''' 5hmC Experiments '''
   Protocol and notes for oxBS (true 5mC quantification): [[Dinh:OxBS_Protocol]]
   Protocol and notes for oxBS (true 5mC quantification): [[Dinh:OxBS_Protocol]]

Revision as of 17:14, 14 July 2015

Daily Lab Notebook

Notebook

Tools

Methylation Sequencing Data Repetiore

  • All methylation data to be stored on genome-miner
  • Data from a publication will be stored under [FirstAuthorLastName][Year]
  • Data from a project will be stored under the project name
  • WGBS (/media/LTS_33T/WGBS_LTS33)
    • Hg19/Ziller2013 - Ziller et al 2013 ( re-analyzed data )
    • Hg19/Heyn2013 - Heyn et al 2013 ( primary data, re-map )
    • Hg19/Xie2013 - Xie et al 2013 ( primary data, re-map )
    • Hg19/NIHRoadMap
    • Hg19/BlueprintProject
    • Hg19/McGillEMC
    • Mm9/
  • RRBS
  • BSPP

Records of all Zhang Lab Methylation data

Dinh:Methylation_Data_Records Dinh:MONOD_Data_Records

Most recent meeting notes

  • [1] Current project meeting notes (Updated May 22, 2015)
  • [2] Current project meeting notes
  • [3] Cancer detection project (Updated April 10, 2014)
  • [4] Senate Exam Meeting (Updated February 28th, 2014)
  • [5] Genome partitioning project (Updated January 16, 2013)
  • [6] 5hmC (CIRM) project (Updated January 3, 2013)

Current Projects and Progress

Dinh's Projects

  • MONOD
  BSPP & SeqCap Mapping statistics: File:150209 SN216 mapping summary statistics.xlsx
  • 5hmC Experiments
  Protocol and notes for oxBS (true 5mC quantification): Dinh:OxBS_Protocol
  Protocol and notes for TAB-PP (true 5hmC quantification): Dinh:TAB_Protocol
  • Probes preparation
  Protocol and notes for preparing probes: Dinh:Probes_Prep
  Protocol and notes for preparing probes: Dinh:Probes_Prep_May2015
  • Stoffel production
  Design
  Plasmid construction - first failed attempt: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2014/NOTES/2014-5-12
   - I repeated Sanger sequencing twice but was unable to get the Stoffel gene in the sequences.
   - One big issue was my plasmid prep (no column) have too much genomic DNA background which M13 primers can amplify.
   - For PCR/Sequencing, I need to use column to purify my plasmids.
  Plasmid construction - try again: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2014/NOTES/2014-6-23
   - I now use NheI digestion site in the middle of the Stoffel gene to screen for my insert. This is much faster than sequencing.
  • Cancer biomarker
  Analysis of GP1 padlock probes capture
  Analysis of MONOD padlock probes capture
  Analysis of RRBS - Dinh:RRBS_MONOD_Analysis/Mapping
  • Genome segmentation
  WGBS data segmentation using N37, Heyn et al (blood), Xie et al (developmental), and Ziller et al (whole tissues, different individuals).
  Mouse WGBS data segmentation using linear regression model and MOABS
  • 5hmC capture and sequencing
  HOTSPOTS460K capture experiments optimization [7]
  HOTSPOTS460K experiments summary [8]
  • bisReadMapper
Developments:
 CpG/ChG/Chh position calling bugs fixed.
 New version of code will use Bowtie2. NGS Mapper ROC curves: http://lh3lh3.users.sourceforge.net/alnROC.shtml
 Run notes: dinh:COMPUTATIONAL/bisReadMapper
UMI procedure: dinh:COMPUTATIONAL/umi_procedure
  • DMR330K probes
re-normalization: [9] Specificity measures, [10] Probes efficiency measures, [11] [12] Resubsetting strategy,
9 Technical Replicates: [13] QC values, [14] [15] [16] Simulation of STDEV, 
Random tagging of probes: [17] [18] [19]
Design new probes: [20] HMM to determine UMR, LMR, and HMR
  • Protocol optimizations:
[21] [22] Capture with 30K, 
[23] Capture with 97KA/B
[24] Multiplexing tests
[25] Multivariate capture with DMR220K
[26] N2-adapter 
[27] [28] BSPP [29] Training
[30] [31] Normalization capture
[32] [33] DMR220K + EXP1-3 Supressor oligos
[34] Design Probes for Single-End sequencing
[35] [36] [37] Circularization of probes
  • Genemapster/Meangenemachine Updates
[38] Cuda EC
[39] Sanger methylation validation
[40] Installed upgrades
[41] New CUDA installation
[42] Test SOAP3 -- doesn't work on our GPU :(
  • Bisulfite Patch PCR (w/Michelle)
[43] Design
[44] Consider SNPs

Projects with Collaborators

  • N37 individual, multiple tissues (Stanford, Billy Li)
    • BSPP (Noi):[45] 1st batch
[46] Genic methylation and expression levels
  • HAPMAP Study (Zhang lab, on grant proposal)
    • BSPP (Noi): [47]
    • WGBS (Alan): ask Alan
Dealing with WGBS data [48] GM12878
Sequence dependent ASM [49] Binomial test and T-test
  • GA - (Glaucoma and optic atrophy?) (Kang Zhang lab)
    • BSPP (Noi): [50] Noi did the experiment while also training two postdocs from Kang's lab.
[51] mQTL on 30 samples, SOM analysis
[52] PCA and HClust
  • Schizophrenia (UCLA, Tina and Dr. Roel)
    • BSPP (Noi): [53] Noi did the experiment while also training Tina over the summer.
Sample identity - males versus females, [54]
Family background substraction, [55]
SibPair using TTest with family null data, [56]
Overlap SibPair with MPO, [57]
SNP Genetic distance plot, [58]
Bis-SNP = more sensitive SNP calling, [59]
  • African Diversity - 48 Methylomes (UPenn collaboration, Sara/Laura)
    • BSPP (Noi):[60] 1st batch [61] 2nd batch, tried to improve QC but they were all too low compared to previously assayed samples.
[62] Analysis with EIGENSTAT software (population structure)
[63] PCA
[64] mQTL
[65] Cleaning and repeat PCA
[66] Checking for reference genome bias
[67] Standardized CpGs quality filter using UPenn48 as an example.
  • 5fC/5caC DIP-seq (University of Northern Carolina Medical School , Yi/Hao/Li)
    • Barcoding and sequencing by Alan:
[68] Genes Region Enrichment analysis, Biotin-labeled dIP 
[69] Antibody dIP
[70] [71][72] Analysis at repeats
[73] 24 sets BOWTIE mapping
[74] [75] [76] [77] BWA PE mapping and peak calling
[78] RNA-seq - repeats mapping
  • Immunogeneticity and reprogramming (Yang Xu lab)
[80] [81] Memory/mutation calling
[82] Compare WGBS
  • Breast Cancer and Diet (Richard, Moores Cancer Center UCSD)
    • Experiments were done in December 2009, January 2010, and February 2010.
[83] Paired Chi-square test 
[84] [85] Compared resequenced datasets with old
[86] [87] mQTL
  • Methylation and metabolic genes
[88] Calculate DMS
  • Memory/Mutation of iPSCs (Salk - Juan Carlos Lab, Sergio)
    • BSPP (Noi): [89] 2nd batch (MSCs, hESCs) [90] 3rd batch, after differentiation
    • BSPP with N2 protocol (Dinh): [91], [92] 1st batch
[93] Memory/mutation calling
[94] CpG localization 
[95] [96] 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